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Submitted URL: http://edge-covid19.edgebioinformatics.org/
Effective URL: https://edge-covid19.edgebioinformatics.org/
Submission: On December 30 via manual from RO — Scanned from DE
Effective URL: https://edge-covid19.edgebioinformatics.org/
Submission: On December 30 via manual from RO — Scanned from DE
Form analysis 5 forms found in the DOM
<form id="edge-run-pipeline-form" autocomplete="off">
<div role="main" id="edge-content-pipeline" class="ui-content edge-content edge-main-page" style="display: block;">
<div class="edge-sponsor-logo">
<img src="images/logo_LANL.png" alt="LANL" style="height:30px">
</div>
<h2>Input Your Sample</h2>
<p class="edge-main-pipeline-input">EDGE requires sequence data files in <b>FASTQ</b> format. EDGE accepts both paired-end and single-end sequence data files. <a href="docs/EDGE_COVID-19_guide.pdf" target="_new" class="ui-link">User Guide</a></p>
<p class="edge-qiime-pipeline-input" style="display: none;">The <a href="https://qiime2.org/" target="_blank" class="ui-link">Qiime2</a> pipeline requires sequence data files in FASTQ format and a
<a href="https://docs.qiime2.org/2019.10/tutorials/metadata/" target="_blank" class="ui-link">mapping file</a>. The sequence file is either paired-end or single-end sequences.Or directory with demultiplexed fastq files. Please see the
<a href="https://edge.readthedocs.io/en/latest/gui.html#run-qiime" target="_new" class="ui-link">documentation</a> for more information.</p>
<p class="edge-targetedngs-pipeline-input" style="display: none;">The <a href="https://chienchilo.bitbucket.io/targetedNGS/" target="_blank" class="ui-link">DETEQT</a> is a pipeline for diagnostic targeted sequencing adjudication. Please see the
<a href="https://edge.readthedocs.io/en/latest/gui.html#run-deteqt" target="_new" class="ui-link">documentation</a> for more information.</p>
<p class="edge-piret-pipeline-input" style="display: none;">The <a href="https://github.com/mshakya/PyPiReT" target="_blank" class="ui-link">PiReT</a> is a pipeline for Reference based Transcriptomics analysis. Please see the
<a href="https://edge.readthedocs.io/en/latest/gui.html#run-piret" target="_new" class="ui-link">documentation</a> for more information.</p>
<div data-role="collapsible-set" class="ui-collapsible-set ui-group-theme-inherit ui-corner-all">
<div data-role="collapsible" id="edge-input-sequence" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" data-collapsed="false" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-first-child">
<h4 class="edge-main-pipeline-input ui-collapsible-heading">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-u ui-btn-icon-left ui-btn-inherit">Input Raw Reads<span class="ui-collapsible-heading-status"> click to collapse contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit" aria-hidden="false">
<div class="ui-body-d ui-content">
<div class="ui-field-contain">
<label for="edge-proj-name">Project/Run Name</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edge-proj-name" id="edge-proj-name" maxlength="30"
placeholder="(required, at 3 but less than 30 characters)"></div>
</div>
<div class="ui-field-contain">
<label for="edge-proj-desc">Description</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edge-proj-desc" id="edge-proj-desc" placeholder="(optional)"></div>
</div>
<div class="ui-field-contain edge-qiime-pipeline-input" style="display: none;">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Amplicon Type</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qiime-at-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">16s (GreenGenes)</label><input type="radio" data-mini="true" name="edge-qiime-at-sw"
id="edge-qiime-at-sw1" value="GreenGenes" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-at-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">16s/18s (SILVA)</label><input type="radio" data-mini="true" name="edge-qiime-at-sw" id="edge-qiime-at-sw2"
value="SILVA"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-at-sw3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">16s V3-V4 (SILVA)</label><input type="radio" data-mini="true" name="edge-qiime-at-sw" id="edge-qiime-at-sw3"
value="SILVA-V3-V4"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-at-sw4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Fungal ITS</label><input type="radio" data-mini="true" name="edge-qiime-at-sw"
id="edge-qiime-at-sw4" value="ITS"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-main-pipeline-input">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Input Source</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-inputS-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">READS / FASTQ</label><input type="radio" data-mini="true" name="edge-inputS-sw"
id="edge-inputS-sw1" value="fastq" checked="checked"></div>
<!--<input type="radio" data-mini="true" name="edge-inputS-sw" id="edge-inputS-sw2" value="fasta">
<label for="edge-inputS-sw2">CONTIGS / FASTA</label>-->
<div class="ui-radio ui-mini"><label for="edge-inputS-sw3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">NCBI SRA</label><input type="radio" data-mini="true" name="edge-inputS-sw" id="edge-inputS-sw3"
value="sra"></div>
</div>
</fieldset>
</div>
<div class="edge-main-pipeline-input">
<div class="ui-field-contain edge-fastq-options" id="edge-fastq-source-block">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Platform</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-fastq-source-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Nanopore</label><input type="radio" data-mini="true" name="edge-fastq-source"
id="edge-fastq-source-sw1" value="nanopore"></div>
<div class="ui-radio ui-mini"><label for="edge-fastq-source-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active">Illumina</label><input type="radio" data-mini="true" name="edge-fastq-source"
id="edge-fastq-source-sw2" value="illumina" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-fastq-source-sw3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">PacBio</label><input type="radio" data-mini="true" name="edge-fastq-source"
id="edge-fastq-source-sw3" value="pacbio"></div>
</div>
</fieldset>
</div>
</div>
<div class="edge-main-pipeline-input">
<div class="ui-field-contain" id="edge-sra-input-block" style="display: none;">
<label for="edge-sra-acc">SRA Accession</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-sra-acc" id="edge-sra-acc" placeholder="ex:SRR11241255"></div>
<p class="edge_tool_note"> (Internet required) Input SRA accessions (comma separate for > 1 input) support studies (SRP*/ERP*/DRP*), experiments (SRX*/ERX*/DRX*), samples (SRS*/ERS*/DRS*), runs (SRR*/ERR*/DRR*), or submissions
(SRA*/ERA*/DRA*). ex: <a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR11241255" target="_blank" class="ui-link">SRR11241255</a></p>
</div>
<div class="ui-field-contain input-type-file" id="edge-fasta-input-block" style="display: none;">
<label for="edge-input-contig-file">Contig Fasta File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-input-contig-file" id="edge-input-contig-file" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="edge-qiime-pipeline-input ui-field-contain ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini" style="display: none;">
<div role="heading" class="ui-controlgroup-label">
<legend>Reads Type</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qiime-rt-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">De-multiplexed Reads Dir</label><input type="radio" data-mini="true"
name="edge-qiime-rt-sw" id="edge-qiime-rt-sw1" value="dedir" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-rt-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Paired Reads</label><input type="radio" data-mini="true" name="edge-qiime-rt-sw" id="edge-qiime-rt-sw2" value="pe">
</div>
<div class="ui-radio ui-mini"><label for="edge-qiime-rt-sw3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Unpaired Reads</label><input type="radio" data-mini="true" name="edge-qiime-rt-sw"
id="edge-qiime-rt-sw3" value="se"></div>
</div>
</fieldset>
<div id="edge-fastq-input-block">
<p class="edge-center edge-main-pipeline-input">Sequencing Reads:</p>
<div id="edge-input-pe-block1" class="edge-input-pe-block">
<div class="ui-field-contain input-type-file">
<label for="edge-input-pe1-1">Pair-1 FASTQ File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-input-pe1[]" id="edge-input-pe1-1" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-input-pe2-1">Pair-2 FASTQ File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-input-pe2[]" id="edge-input-pe2-1" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
<a href="#" class="btnDel-edge-input-pe ui-link ui-btn ui-icon-delete ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="delete" data-iconpos="notext" role="button">Delete</a>
</div>
</div>
</div>
<p class="edge-center edge-main-pipeline-input">and/or</p>
<div id="edge-input-se-block1" class="ui-field-contain input-type-file edge-input-se-block">
<label for="edge-input-se-1">Single-end FASTQ File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-input-se[]" id="edge-input-se-1" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
<a href="#" class="btnDel-edge-input ui-link ui-btn ui-icon-delete ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="delete" data-iconpos="notext" role="button">Delete</a>
</div>
</div>
</div>
<div class="edge-qiime-pipeline-input edge-targetedngs-pipeline-input edge-piret-pipeline-input" style="display: none;">
<div id="edge-qiime-pipeline-dir-input" class="ui-field-contain input-type-file">
<label for="edge-qiime-reads-dir-input">Directory<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-qiime-reads-dir-input" id="edge-qiime-reads-dir-input" placeholder="absolute dir path/select dir"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">Dir</a>
</div>
</div>
</div>
<div class="edge-qiime-pipeline-input edge-targetedngs-pipeline-input edge-piret-pipeline-input" style="display: none;">
<div id="edge-qiime-pipeline-input-block1" class="ui-field-contain input-type-file edge-qiime-pipeline-input-block">
<label for="edge-qiime-mapping-file-input-1">Metadata Mapping
File<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-qiime-mapping-file-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-qiime-mapping-file-input[]" id="edge-qiime-mapping-file-input-1"
placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
<a href="#" class="btnDel-edge-input ui-link ui-btn ui-icon-delete ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="delete" data-iconpos="notext" role="button">Delete</a>
</div>
</div>
</div>
<div class="edge-targetedngs-pipeline-input" style="display: none;">
<div class="ui-field-contain input-type-file">
<label for="edge-targetedngs-ref-file">Targeted Amplicon
References<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-targetedngs-ref-file-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-targetedngs-ref-file" id="edge-targetedngs-ref-file" placeholder="absolute FASTA file path/select file">
</div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<div class="edge-right">|<a href="#" id="edge-input-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-input-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain btnAdd-edge-input">
<a href="#" id="btnAdd-edge-input-pe" data-theme="b" data-role="button" data-inline="true" data-mini="true" data-icon="plus" data-iconpos="right" class="ui-link ui-btn ui-btn-b ui-icon-plus ui-btn-icon-right ui-btn-inline ui-shadow ui-corner-all ui-mini" role="button">Add Paired-end Input</a>
<a href="#" id="btnAdd-edge-input-se" data-theme="b" data-role="button" data-inline="true" data-mini="true" data-icon="plus" data-iconpos="right" class="ui-link ui-btn ui-btn-b ui-icon-plus ui-btn-icon-right ui-btn-inline ui-shadow ui-corner-all ui-mini" role="button">Add Single-end Input</a>
<a href="#" id="btnAdd-edge-qiime-mapping-file" class="edge-qiime-pipeline-input ui-link ui-btn ui-btn-b ui-icon-plus ui-btn-icon-right ui-btn-inline ui-shadow ui-corner-all ui-mini" data-theme="b" data-role="button" data-inline="true" data-mini="true" data-icon="plus" data-iconpos="right" role="button" style="display: none;">Add Mapping File Field</a>
</div>
<div class="ui-field-contain">
<label for="edge-proj-desc">Use # of CPUs</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edge-proj-cpu" id="edge-proj-cpu" value="1"></div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-input-config">Config File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-input-config" id="edge-input-config" placeholder="(optional) absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<p class="edge_tool_note">Your customized parameters can be used again. You can utilize the file selector above to upload a standard config file generated by EDGE bioinformatics.</p>
</div>
</div>
</div>
</div>
<div id="edge-batch-input" class="edge-main-pipeline-input ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed ui-last-child" data-role="collapsible" data-collapsed-icon="carat-d"
data-expanded-icon="carat-u" data-collapsed="true">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">Batch Project Submission<span class="ui-collapsible-heading-status"> click to expand contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<p class="edge_tool_note">Run EDGE with Multiple projects using a tools set configuration. Click <a href="data/BatchExcelExample.xlsx" download="" target="_blank" class="ui-link"> Download [Sample File]</a> to see the example. </p>
<div id="edge-batch-input-block1" class="edge-batch-input">
<div class="ui-field-contain input-type-file">
<label for="edge-batch-input-excel-1">Batch Excel
File<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" for="edge-batch-input-block1" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-batch-input-excel" id="edge-batch-input-excel-1" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- gisaid sample metadata -->
<div id="edge-sample-metadata" class="edge-main-pipeline-input">
<div data-role="collapsible" id="edge-input-metadata" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" data-collapsed="true"
class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed">
<h4 class="edge-main-pipeline-input ui-collapsible-heading ui-collapsible-heading-collapsed">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">Input Metadata<span class="ui-collapsible-heading-status"> click to expand contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<div class="ui-corner-all custom-corners">
<div class="ui-corner-all custom-corners">
<div class="ui-bar ui-bar-d">
<b><em>Virus detail</em></b>
</div>
<div class="ui-body ui-body-a ui-corner-all">
<div class="ui-field-contain">
<label for="metadata-virus-name">Virus name</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input type="text" id="metadata-virus-name" name="metadata-virus-name" placeholder="hCoV-19/Country/Identifier/2020" class="metadata-input"></div>
</div>
<div class="ui-field-contain">
<label for="metadata-virus-passage">Passage details/history</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input type="text" id="metadata-virus-passage" name="metadata-virus-passage" placeholder="Example: Original, Vero" class="metadata-input"></div>
</div>
</div>
</div>
<br><br>
<div class="ui-corner-all custom-corners">
<div class="ui-bar ui-bar-d">
<b><em>Sample information</em></b>
</div>
<div class="ui-body ui-body-a ui-corner-all">
<div class="ui-field-contain">
<label for="metadata-sample-collection-date">Collection date</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-role="date" data-mini="true" data-clear-btn="false" name="metadata-sample-collection-date" id="metadata-sample-collection-date"
placeholder="Example: 2020-03-27, 2020-03 (collection in March, day unknown), 2020 (month and day unknown)" maxlength="30" class="metadata-input metadata-input-date hasDatepicker"></div>
</div>
<div class="ui-field-contain">
<label>Location</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input name="metadata-sample-location" id="metadata-sample-location" type="text" placeholder="Continent/Country/Region" class="metadata-input"></div>
</div>
<div class="ui-field-contain">
<label>Host</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input name="metadata-sample-host" id="metadata-sample-host" type="text"
placeholder="Example: Human, Environment, Canine, Manis javanica, Rhinolophus affinis, unknown" class="metadata-input"></div>
</div>
<div class="ui-field-contain">
<label>Gender</label>
<div class="ui-select ui-mini">
<a href="#" role="button" id="metadata-sample-gender-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span class="metadata-input">Select Gender</span></a><select
name="metadata-sample-gender" id="metadata-sample-gender" data-mini="true" data-native-menu="false" class="metadata-input" tabindex="-1">
<option value="" data-placeholder="true">Select Gender</option>
<option value="Male">Male</option>
<option value="Female">Female</option>
<option value="Other">Other</option>
<option value="Unknown">Unknown</option>
</select>
<div style="display: none;" id="metadata-sample-gender-listbox-placeholder"><!-- placeholder for metadata-sample-gender-listbox --></div>
</div>
</div>
<div class="ui-field-contain">
<label>Patient age</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input name="metadata-sample-age" id="metadata-sample-age" type="text" placeholder="Example: 65, 7 monthis, or unknown" class="metadata-input"></div>
</div>
<div class="ui-field-contain">
<label>Patient status</label>
<div class="ui-select ui-mini">
<a href="#" role="button" id="metadata-sample-status-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span class="metadata-input">Select Status</span></a><select
name="metadata-sample-status" id="metadata-sample-status" data-mini="true" data-native-menu="false" class="metadata-input" tabindex="-1">
<option value="" data-placeholder="true">Select Status</option>
<option value="Hospitalized">Hospitalized</option>
<option value="Released">Released</option>
<option value="Live">Live</option>
<option value="Deceased">Deceased</option>
<option value="Unknown">Unknown</option>
</select>
<div style="display: none;" id="metadata-sample-status-listbox-placeholder"><!-- placeholder for metadata-sample-status-listbox --></div>
</div>
</div>
<div class="ui-field-contain">
<label>Sequencing Technology</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input name="metadata-sample-sequencing-tech" id="metadata-sample-sequencing-tech" type="text"
placeholder="e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc." class="metadata-input"></div>
</div>
</div>
</div>
<br><br>
</div>
</div>
</div>
</div>
<!-- END gisaid sample metadata -->
<p></p>
<h2 class="edge-main-pipeline-input">Choose Processes / Analyses</h2>
<p id="edge-runEDGE-modules-desc" class="edge-main-pipeline-input">EDGE provides many modules to do various analyses. You can choose to run or skip a specific process. Parameters/options are provided for most of the analyses. You can click here
to <a href="#" id="edge-all-on-btn" class="ui-link">turn all on</a>, <a href="#" id="edge-all-exp-btn" class="ui-link">expand all sections</a> or <a href="#" id="edge-all-close-btn" class="ui-link">close all sections</a>. </p>
<div id="edge-runEDGE-modules" class="edge-main-pipeline-input">
<div id="edge-runEDGE-pp" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="edge-fastq-options ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-pp-sw" name="edge-pp-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0">Off</option><option value="1" selected="TRUE">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 100%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 0%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="1" aria-valuetext="On" title="On" aria-labelledby="edge-pp-sw-label" style="left: 100%;"></a>
</div>
</div>
<label for="edge-pp-sw" id="edge-pp-sw-label">Pre-processing</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<div class="edge-tabs">
<div class="ui-grid-b">
<div class="ui-block-a"><a href="#" data-id="edge-qc-parameters" class="ui-btn ui-mini ui-btn-active">Quality Trim and Filter</a></div>
<div class="ui-block-b"><a href="#" data-id="edge-joinpe-parameters" class="ui-btn ui-mini">Stitch Paired-End Reads</a></div>
<div class="ui-block-c"><a href="#" data-id="edge-hostrm-parameters" class="ui-btn ui-mini">Host Removal</a></div>
</div>
</div>
<div id="edge-qc-parameters">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Run Quality Trim and Filter</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qc-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-qc-sw" id="edge-qc-sw1" value="1"
checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qc-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-qc-sw" id="edge-qc-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Quality Offset<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qc-phred-offset1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">AutoCheck</label><input type="radio" data-mini="true" name="edge-qc-phred-offset"
id="edge-qc-phred-offset1" value="0" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qc-phred-offset2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Phred+33</label><input type="radio" data-mini="true" name="edge-qc-phred-offset" id="edge-qc-phred-offset2"
value="33"></div>
<div class="ui-radio ui-mini"><label for="edge-qc-phred-offset3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Phred+64</label><input type="radio" data-mini="true" name="edge-qc-phred-offset"
id="edge-qc-phred-offset3" value="64"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<label for="edge-qc-q">Trim Quality Level<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="qc-q-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-q" id="edge-qc-q" data-mini="true" data-clear-btn="true"
value="20"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-qc-avgq">Average Quality Cutoff<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-avgq" id="edge-qc-avgq" data-mini="true" data-clear-btn="true"
value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-qc-minl">Minimum Read Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-minl" id="edge-qc-minl" data-mini="true" data-clear-btn="true"
value="50"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-qc-n">"N" Base Cutoff<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-n" id="edge-qc-n" data-mini="true" data-clear-btn="true"
value="10"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-qc-lc" id="edge-qc-lc-label">Low Complexity
Filter<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-qc-lc" id="edge-qc-lc" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.85" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini" aria-disabled="false">
<div class="ui-slider-bg ui-btn-active" style="width: 85%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.85" aria-valuetext="0.85" title="0.85" aria-labelledby="edge-qc-lc-label" style="left: 85%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Trim Sequencing Primers<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-porechop-sw1" title="ARTIC V1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">V1</label><input type="radio" data-mini="true" name="edge-porechop-sw"
id="edge-porechop-sw1" value="artic_ncov2019_primer_schemes_V1"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw2" title="ARTIC V2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">V2</label><input type="radio" data-mini="true" name="edge-porechop-sw" id="edge-porechop-sw2"
value="artic_ncov2019_primer_schemes_V2"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw3" title="ARTIC V3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">V3</label><input type="radio" data-mini="true" name="edge-porechop-sw" id="edge-porechop-sw3"
value="artic_ncov2019_primer_schemes_V3"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw4" title="ARTIC V4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">V4</label><input type="radio" data-mini="true" name="edge-porechop-sw" id="edge-porechop-sw4"
value="artic_ncov2019_primer_schemes_V4"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw5" title="SC2_200324" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">CDC</label><input type="radio" data-mini="true" name="edge-porechop-sw" id="edge-porechop-sw5"
value="SC2_200324"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw6" title="swift_primer_schemes_v2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">SWIFT</label><input type="radio" data-mini="true" name="edge-porechop-sw"
id="edge-porechop-sw6" value="swift_primer_schemes_v2"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw7" title="sarscov2_freed_primers" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Freed</label><input type="radio" data-mini="true" name="edge-porechop-sw"
id="edge-porechop-sw7" value="Pacbio_sarscov2_freed_primers"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw8" title="Varskip_V1a" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Varskip_V1a</label><input type="radio" data-mini="true" name="edge-porechop-sw"
id="edge-porechop-sw8" value="NEB_VarSkip.scheme"></div>
<div class="ui-radio ui-mini"><label for="edge-porechop-sw9" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="edge-porechop-sw"
id="edge-porechop-sw9" value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Primer Trim Method<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-align-trim-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Align Trim</label><input type="radio" data-mini="true"
name="edge-r2g-align-trim-sw" id="edge-r2g-align-trim-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-align-trim-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">FaQCs</label><input type="radio" data-mini="true" name="edge-r2g-align-trim-sw"
id="edge-r2g-align-trim-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-r2g-align-trim-bed-file">Primer BED<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: auto;"><input data-mini="true" name="edge-r2g-align-trim-bed-file" id="edge-r2g-align-trim-bed-file" type="text"
placeholder="(optional) absolute file path/select file"></div>
<div class="edge-file-selector" style="pointer-events: auto;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain input-type-file" style="display: none;">
<label for="edge-qc-adapter">Primer FASTA</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: auto;"><input data-mini="true" name="edge-qc-adapter" id="edge-qc-adapter" type="text"
placeholder="(optional) absolute file path/select file"></div>
<div class="edge-file-selector" style="pointer-events: auto;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Trim polyA</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qc-polyA1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">On</label><input type="radio" data-mini="true" name="edge-qc-polyA" id="edge-qc-polyA1" value="1">
</div>
<div class="ui-radio ui-mini"><label for="edge-qc-polyA2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="edge-qc-polyA" id="edge-qc-polyA2"
value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<!--<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal">
<legend>phiX Filter</legend>
<input type="radio" data-mini="true" name="edge-qc-phix" id="edge-qc-phix1" value="1">
<label for="edge-qc-phix1">On</label>
<input type="radio" data-mini="true" name="edge-qc-phix" id="edge-qc-phix2" value="0" checked="checked">
<label for="edge-qc-phix2">Off</label>
</fieldset>
</div>-->
<div class="ui-field-contain">
<label for="edge-qc-5end">Cut #bp from 5'-end</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-5end" id="edge-qc-5end" data-mini="true" data-clear-btn="true"
value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-qc-3end">Cut #bp from 3'-end</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-qc-3end" id="edge-qc-3end" data-mini="true" data-clear-btn="true"
value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div> <!--edge-qc-parameters-->
<div id="edge-joinpe-parameters" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Run Stitch PE Reads</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-joinpe-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-joinpe-sw" id="edge-joinpe-sw1" value="1">
</div>
<div class="ui-radio ui-mini"><label for="edge-joinpe-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-joinpe-sw" id="edge-joinpe-sw2"
value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<label for="edge-joinpe-maxdiff">N-percent Max Difference</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-joinpe-maxdiff" id="edge-joinpe-maxdiff" data-mini="true" data-clear-btn="true" value="8"
max="100"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-joinpe-minoverlap">N-minimum Overlap</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-joinpe-minoverlap" id="edge-joinpe-minoverlap" data-mini="true" data-clear-btn="true" value="6"
max="150"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Use joined PE reads only<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-joinpe-usejoined-only1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-joinpe-usejoined-only"
id="edge-joinpe-usejoined-only1" value="1"></div>
<div class="ui-radio ui-mini"><label for="edge-joinpe-usejoined-only2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true"
name="edge-joinpe-usejoined-only" id="edge-joinpe-usejoined-only2" value="0" checked="checked"></div>
</div>
</fieldset>
</div>
</div>
<div id="edge-hostrm-parameters" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Human Host Removal<a href="#" class="tooltip ui-btn ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn ui-nodisc-icon tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-hostrm-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-hostrm-sw" id="edge-hostrm-sw1"
value="human_ref_GRCh38_all"></div>
<div class="ui-radio ui-mini"><label for="edge-hostrm-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-hostrm-sw" id="edge-hostrm-sw2"
value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<!--<div class="ui-field-contain input-type-file">
<label for="edge-hostrm-file-fromlist">Select Genome(s)</label>
<select id="edge-hostrm-file-fromlist" data-mini="true" name="edge-hostrm-file-fromlist" data-native-menu="false" multiple="multiple">
<option disabled>Select host genome(s)...</option>
</select>
</div>
<p class="edge-center">and</p>-->
<div class="ui-field-contain input-type-file">
<label for="edge-hostrm-file">Additional Host FASTA File<a href="#" class="tooltip ui-btn ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn ui-nodisc-icon tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: auto;"><input type="text" name="edge-hostrm-file" id="edge-hostrm-file" data-mini="true"
placeholder="absolute file path/select file"></div>
<div class="edge-file-selector" style="pointer-events: auto;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-hostrm-similarity">Similarity (%)<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-hostrm-similarity" id="edge-hostrm-similarity" data-mini="true" data-clear-btn="true"
value="80"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<!--
<div class="ui-field-contain">
<label for="edge-hostrm-minlen">Minimum Alignment Length</label>
<input type="number" name="edge-hostrm-minlen" id="edge-hostrm-minlen" data-mini="true" data-clear-btn="true" value="50">
</div>
-->
</div><!--edge-hostr-parameters-->
</div>
</div>
<div id="edge-runEDGE-aa" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-assembly-sw" name="edge-assembly-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0" selected="TRUE">Off</option><option value="1">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 0%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 100%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0" aria-valuetext="Off" title="Off" aria-labelledby="edge-assembly-sw-label" style="left: 0%;"></a>
</div>
</div>
<label for="edge-assembly-sw" id="edge-assembly-sw-label">Assembly and Annotation</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<div class="edge-tabs">
<div class="ui-grid-b">
<div class="ui-block-a edge-fastq-options"><a href="#" data-id="edge-assembly-parameters" class="ui-btn ui-mini ui-btn-active"> Assembly</a></div>
<div class="ui-block-b"><a href="#" data-id="edge-annotation-parameters" class="ui-btn ui-mini">Annotation</a></div>
<div class="ui-block-c" style="display: none;"><a href="#" data-id="edge-binning-parameters" class="ui-btn ui-mini">Binning</a></div>
</div>
</div>
<div id="edge-assembly-parameters" class="edge-fastq-options">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Bypass Assembly And Use Pre-assembled Contigs</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-assembled-contig1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" name="edge-assembled-contig-sw" id="edge-assembled-contig1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-assembled-contig2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" name="edge-assembled-contig-sw"
id="edge-assembled-contig2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file" id="edge-assembled-conti-file-div" style="display: none;">
<label for="edge-assembled-contig-file">Contig Fasta File</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-assembled-contig-file" id="edge-assembled-contig-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain" id="edge-assembler-sw">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Assembler</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-assembler1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">IDBA_UD</label><input type="radio" name="edge-assembler" id="edge-assembler1"
value="idba_ud" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-assembler2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">SPAdes</label><input type="radio" name="edge-assembler" id="edge-assembler2" value="spades" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-assembler3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">MEGAHIT</label><input type="radio" name="edge-assembler" id="edge-assembler3" value="megahit" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-assembler4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">UniCycler</label><input type="radio" name="edge-assembler" id="edge-assembler4" value="unicycler" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-assembler5" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">LRASM</label><input type="radio" name="edge-assembler" id="edge-assembler5" value="lrasm" disabled="">
</div>
</div>
</fieldset>
</div>
<div id="edge-unicycler-parameters" class="edge-assembler-parameters" style="display: none;">
<p class="edge_tool_note"><a href="https://github.com/rrwick/Unicycler" target="_blank" class="ui-link">Unicycler</a> is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a
SPAdes-optimise. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.</p>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Bridging mode<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-unicycler-mode1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Normal</label><input type="radio" name="edge-unicycler-mode"
id="edge-unicycler-mode1" value="normal" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-unicycler-mode2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Conservative</label><input type="radio" name="edge-unicycler-mode" id="edge-unicycler-mode2"
value="conservative" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-unicycler-mode3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Bold</label><input type="radio" name="edge-unicycler-mode" id="edge-unicycler-mode3"
value="bold" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-unicycler-lreads-file">Long Reads Fasta/q</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-unicycler-lreads-file" id="edge-unicycler-lreads-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain"><label for="edge-unicycler-min-lreads">Minimum Long Reads Cutoff (bp)</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-unicycler-min-lreads" id="edge-unicycler-min-lreads"
value="2000" min="1000" disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div>
<div id="edge-lrasm-parameters" class="edge-assembler-parameters" style="display: none;">
<p class="edge_tool_note"><a href="https://gitlab.com/chienchi/long_read_assembly" target="_blank" class="ui-link">LRASM</a> is designed for long noise reads such as reads from Nanopore and it assemble fastq/fasta formatted reads using
miniasm/wtdbg2/flye and use racon to perform consensus.</p>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Algorithm<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-lrasm-algorithm-tooltip" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-lrasm-algorithm1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">miniasm</label><input type="radio" name="edge-lrasm-algorithm"
id="edge-lrasm-algorithm1" value="miniasm" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-lrasm-algorithm2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">wtdbg2</label><input type="radio" name="edge-lrasm-algorithm" id="edge-lrasm-algorithm2" value="wtdbg2"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-lrasm-algorithm3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">flye</label><input type="radio" name="edge-lrasm-algorithm" id="edge-lrasm-algorithm3" value="flye"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-lrasm-algorithm4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">metaFlye</label><input type="radio" name="edge-lrasm-algorithm" id="edge-lrasm-algorithm4"
value="metaflye" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Error Correction<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-lrasm-ec1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" name="edge-lrasm-ec" id="edge-lrasm-ec1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-lrasm-ec2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" name="edge-lrasm-ec" id="edge-lrasm-ec2" value="0"
checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Preset</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-lrasm-preset1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Nanopore</label><input type="radio" name="edge-lrasm-preset"
id="edge-lrasm-preset1" value="ont" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-lrasm-preset2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Pacbio</label><input type="radio" name="edge-lrasm-preset" id="edge-lrasm-preset2" value="pb"
disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain"><label for="edge-lrasm-num-consensus">Num of Iteration of Consensus </label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-lrasm-num-consensus" id="edge-lrasm-num-consensus" max="10"
value="3" disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div>
<div id="edge-idba-parameters" class="edge-assembler-parameters">
<p class="edge_tool_note"><a href="https://github.com/loneknightpy/idba" target="_blank" class="ui-link">IDBA_UD</a> performs well on isolates as well as metagenomes but it may not work well on very large genomes.</p>
<div class="ui-field-contain"><label for="edge-assembly-mink">Minimum Kmer Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-assembly-mink" id="edge-assembly-mink" value="31"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain"><label for="edge-assembly-maxk">Maximum Kmer Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-assembly-maxk" id="edge-assembly-maxk" value="121"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain"><label for="edge-assembly-step">Step Size</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-assembly-step" id="edge-assembly-step" value="20"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div>
<div id="edge-spades-parameters" class="edge-assembler-parameters" style="display: none;">
<p class="edge_tool_note"><a href="https://github.com/ablab/spades" target="_blank" class="ui-link">SPAdes</a> performs well on isolates as well as single cell data but it may not work on larger genomes, and it takes more computational
resource. PacBio CLR and Oxford Nanopore reads are used for gap closure and repeat resolution.</p>
<div class="ui-field-contain">
<label for="edge-spades-algorithm">Algorithm</label>
<div class="ui-select ui-mini"><a href="#" role="button" id="edge-spades-algorithm-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span>Default</span></a><select
id="edge-spades-algorithm" data-mini="true" name="edge-spades-algorithm" data-native-menu="false" tabindex="-1">
<option value="default">Default</option>
<option value="singlecell">Single-cell (MDA)</option>
<option value="metagenome">Metagenome (metaSPAdes)</option>
<option value="plasmid">Plasmids (plasmidSPAdes)</option>
<option value="rna">RNA (rnaSPAdes)</option>
</select>
<div style="display: none;" id="edge-spades-algorithm-listbox-placeholder"><!-- placeholder for edge-spades-algorithm-listbox --></div>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-spades-pacbio-file">Pacbio Subreads Fasta/q</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-spades-pacbio-file" id="edge-spades-pacbio-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-spades-nanopore-file">Nanopore Reads Fasta/q</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-spades-nanopore-file" id="edge-spades-nanopore-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<div id="edge-megahit-parameters" class="edge-assembler-parameters" style="display: none;">
<p class="edge_tool_note"><a href="https://github.com/voutcn/megahit" target="_blank" class="ui-link">MEGAHIT</a> is an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph which
achieves low memory assembly. </p>
<div class="ui-field-contain">
<label
for="edge-megahit-preset">Preset<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-megahit-preset-l" style="display: none;"></a></label>
<div class="ui-select ui-mini"><a href="#" role="button" id="edge-megahit-preset-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span>meta</span></a><select
id="edge-megahit-preset" data-mini="true" name="edge-megahit-preset" data-native-menu="false" tabindex="-1">
<option value="meta">meta</option>
<option value="meta-sensitive">meta-sensitive</option>
<option value="meta-large">meta-large</option>
</select>
<div style="display: none;" id="edge-megahit-preset-listbox-placeholder"><!-- placeholder for edge-megahit-preset-listbox --></div>
</div>
</div>
</div>
<div class="ui-field-contain"><label for="edge-assembly-minc">Minimum Contig Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-assembly-minc" id="edge-assembly-minc" value="200"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain" id="edge-r2c-aligner-sw">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Validation Aligner<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2c-aligner1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Bowtie 2</label><input type="radio" name="edge-r2c-aligner" id="edge-r2c-aligner1" value="bowtie"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-r2c-aligner2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active">BWA mem</label><input type="radio" name="edge-r2c-aligner" id="edge-r2c-aligner2" value="bwa"
checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-r2c-aligner3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Minimap2</label><input type="radio" name="edge-r2c-aligner" id="edge-r2c-aligner3" value="minimap2"
disabled=""></div>
</div>
</fieldset>
</div>
<div class="edge-right">|<a href="#" id="edge-r2c-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-r2c-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain">
<label for="edge-r2c-aligner-options">Aligner
Options<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn edge-aligner-options tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edge-r2c-aligner-options" id="edge-r2c-aligner-options" placeholder="(optional)"
disabled=""></div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Extract Unmapped/Unassembled Reads</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2c-getunmapped1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" name="edge-r2c-getunmapped-sw" id="edge-r2c-getunmapped1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-r2c-getunmapped2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" name="edge-r2c-getunmapped-sw"
id="edge-r2c-getunmapped2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div>
</div> <!-- edge-assembly-parameters-->
<div id="edge-annotation-parameters" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Annotation</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-anno-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-anno-sw" id="edge-anno-sw1" value="1"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-anno-sw" id="edge-anno-sw2"
value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<p class="edge_tool_note">EDGE will use <a href="http://ratt.sourceforge.net/" target="_new" class="ui-link">RATT</a> to transfer the annotation from the reference genome,
<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2/" target="_new" class="ui-link">NC_045512.2</a>.</p>
<div class="ui-field-contain"><label for="edge-anno-size-cut">Minimum Contig Length for Annotation</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-anno-size-cut" id="edge-anno-size-cut" value="700"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain" style="display: none;">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Annotation Tool<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-anno-tool1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Prokka</label><input type="radio" name="edge-anno-tool" id="edge-anno-tool1" value="prokka"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-tool2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">RATT</label><input type="radio" name="edge-anno-tool" id="edge-anno-tool2" value="RATT"
checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div id="edge-anno-kingdom" class="ui-field-contain" style="display: none;">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Specify Kingdom<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-anno-kingdom1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Archaea</label><input type="radio" name="edge-anno-kingdom" id="edge-anno-kingdom1"
value="Archaea" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-kingdom2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Bacteria</label><input type="radio" name="edge-anno-kingdom" id="edge-anno-kingdom2" value="Bacteria"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-kingdom3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Mitochondria</label><input type="radio" name="edge-anno-kingdom" id="edge-anno-kingdom3" value="Mitochondria"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-kingdom4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active">Viruses</label><input type="radio" name="edge-anno-kingdom" id="edge-anno-kingdom4" value="Viruses"
checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-kingdom5" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Metagenome</label><input type="radio" name="edge-anno-kingdom" id="edge-anno-kingdom5"
value="Metagenome" disabled=""></div>
</div>
</fieldset>
</div>
<div id="edge-anno-kegg" class="ui-field-contain" style="display: none;">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>KEGG Pathway View<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-anno-kegg-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-anno-kegg-sw" id="edge-anno-kegg-sw1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-anno-kegg-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-anno-kegg-sw"
id="edge-anno-kegg-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div id="edge-anno-source" style="display: none;">
<div class="ui-field-contain input-type-file">
<label for="edge-anno-source-file">Annotation Source
Genbank<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-anno-source-file" id="edge-anno-source-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<!-- <div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal">
<legend>Secondary Metabolite Analysis<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn" title="EDGE use antiSMASH v4.1.0 for the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes."></a></legend>
<input type="radio" data-mini="true" name="edge-sma-sw" id="edge-sma-sw1" value="1">
<label for="edge-sma-sw1">Yes</label>
<input type="radio" data-mini="true" name="edge-sma-sw" id="edge-sma-sw2" value="0" checked="checked">
<label for="edge-sma-sw2">No</label>
</fieldset>
</div>
-->
<div class="ui-grid-a edge-tool-parameters" id="edge-sma-parameters" style="display: none;">
<p class="edge-center edge_tool_note">Secondary Metabolite Analysis Parameters</p>
<div class="ui-block-a">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Taxon</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-taxon-1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Bacteria</label><input type="radio" data-mini="true" name="antismash-taxon"
id="edge-sma-taxon-1" value="bacteria" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-taxon-2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Fungi</label><input type="radio" data-mini="true" name="antismash-taxon" id="edge-sma-taxon-2"
value="fungi" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-a">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Known ClusterBlast<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-kcb-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-knownclusterblast"
id="edge-sma-kcb-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-kcb-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-knownclusterblast"
id="edge-sma-kcb-sw2" value="0" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-b">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Sub ClusterBlast<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-scb-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-subclusterblast"
id="edge-sma-scb-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-scb-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-subclusterblast"
id="edge-sma-scb-sw2" value="0" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-a">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>smCoG analysis<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-smcogs-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-smcogs"
id="edge-sma-smcogs-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-smcogs-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-smcogs"
id="edge-sma-smcogs-sw2" value="0" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-b">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Active Site Finder<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-asf-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-asf"
id="edge-sma-asf-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-asf-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-asf" id="edge-sma-asf-sw2"
value="0" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-a">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>ClusterBlast<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-cb-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-clusterblast" id="edge-sma-cb-sw1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-cb-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-clusterblast"
id="edge-sma-cb-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-b">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Whole-genome PFAM analysis<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-wgpa-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-fullhmm" id="edge-sma-wgpa-sw1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-wgpa-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-fullhmm"
id="edge-sma-wgpa-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-a antismash-bacteria-only-option">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Detect TTA codons<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-tta-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-tta" id="edge-sma-tta-sw1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-tta-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-tta"
id="edge-sma-tta-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-block-a antismash-fungi-only-option" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Cluster-border prediction based on transcription factor binding sites
(CASSIS)<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-sma-cassis-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">On</label><input type="radio" data-mini="true" name="antismash-cassis"
id="edge-sma-cassis-sw1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-sma-cassis-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Off</label><input type="radio" data-mini="true" name="antismash-cassis"
id="edge-sma-cassis-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div>
</div>
<div class="edge-right">|<a href="#" id="edge-anno-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-anno-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain input-type-file" style="display: none;">
<label for="edge-anno-hmm-file">Trusted HMM for Prokka<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-anno-hmm-file" id="edge-anno-hmm-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
</div> <!-- edge-annotation-parameters -->
<div id="edge-binning-parameters" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Binning</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-binning-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-binning-sw" id="edge-binning-sw1"
value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-binning-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-binning-sw"
id="edge-binning-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain"><label for="edge-binning-size-cut">Minimum Contig Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-binning-size-cut" id="edge-binning-size-cut" value="1000"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain"><label for="edge-binning-max-itr">Maximum EM Algorithm Iteration</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-binning-max-itr" id="edge-binning-max-itr" value="50"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-binning-prob" id="edge-binning-prob-label">EM
Probability<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-binning-prob" id="edge-binning-prob" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.90" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input mobile-slider-disabled" disabled="">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini ui-state-disabled" aria-disabled="true">
<div class="ui-slider-bg ui-btn-active" style="width: 90%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.9" aria-valuetext="0.9" title="0.9" aria-labelledby="edge-binning-prob-label" style="left: 90%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain" id="edge-binning-marker-sw">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Marker Gene Sets<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-binning-markerset1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">107</label><input type="radio" name="edge-binning-markerset"
id="edge-binning-markerset1" value="107" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-binning-markerset2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">40</label><input type="radio" name="edge-binning-markerset" id="edge-binning-markerset2"
value="40" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-binning-abund-file">Abundance
File<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-binning-abund-file-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-binning-abund-file" id="edge-binning-abund-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>CheckM<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-binning-checkM-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-binning-checkM-sw"
id="edge-binning-checkM-sw1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-binning-checkM-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-binning-checkM-sw"
id="edge-binning-checkM-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
</div><!-- edge-binning-parameters -->
</div>
</div>
<div id="edge-runEDGE-rba" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content">
<h4 class="ui-collapsible-heading"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-btn-icon-left ui-btn-inherit ui-icon-carat-u">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-btn-icon-left ui-btn-inherit ui-icon-carat-u">
<select id="edge-ref-sw" name="edge-ref-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0">Off</option><option value="1" selected="TRUE">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-btn-icon-left ui-btn-inherit ui-icon-carat-u"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 100%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 0%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-btn-icon-left ui-btn-inherit ui-icon-carat-u"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="1" aria-valuetext="On" title="On" aria-labelledby="edge-ref-sw-label" style="left: 100%;"></a>
</div>
</div>
<label for="edge-ref-sw" id="edge-ref-sw-label">Reference-Based SARS-CoV-2 Genome Analysis</label>
</div>
<span class="ui-collapsible-heading-status"> click to collapse contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit" aria-hidden="false">
<!--<p class="edge_tool_note">EDGE will use <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2/" target="_new">NC_045512.2</a> as reference. You can add one or more reference genome files, EDGE will turn on the analysis of the reads/contigs mapping to reference and JBrowse reference track generation. Given reference genomes in genbank format, EDGE will also turn on variant analysis.</p>-->
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Preselected <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2/" target="_new" class="ui-link">NCBI RefSeq</a> Reference
Genome<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-selected-ref-input-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true"
name="edge-selected-ref-input-sw" id="edge-selected-ref-input-sw1" value="NC_045512.2" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-selected-ref-input-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-selected-ref-input-sw"
id="edge-selected-ref-input-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-ref-file-fromlist">Select Additional GenBank Reference Genome(s)
(Optional)<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-ref-file-fromlist-tooltip" style="display: none;"></a></label>
<div class="ui-select ui-mini" style="pointer-events: auto;">
<a href="#" role="button" id="edge-ref-file-fromlist-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow ui-li-has-count"><span>Select additional reference genome(s)...</span><span class="ui-li-count ui-body-inherit" style="display: none;">0</span></a><select
id="edge-ref-file-fromlist" data-mini="true" name="edge-ref-file-fromlist" data-native-menu="false" multiple="multiple" tabindex="-1">
<option disabled="" data-placeholder="true">Select additional reference genome(s)...</option>
</select>
<div style="display: none; pointer-events: auto;" id="edge-ref-file-fromlist-listbox-placeholder"><!-- placeholder for edge-ref-file-fromlist-listbox --></div>
</div>
</div>
<!--<p class="edge-center">and/or</p>-->
<div id="edge-ref-file-block1" class="ui-field-contain input-type-file edge-ref-file-block">
<label for="edge-ref-file-1">Extra Reference Genome (Optional)</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: auto;"><input type="text" data-mini="true" name="edge-ref-file[]" id="edge-ref-file-1"
placeholder="absolute FASTA/GenBank file path/select file"></div>
<div class="edge-file-selector" style="pointer-events: auto;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
<a href="#" class="btnAdd-edge-ref-file ui-link ui-btn ui-icon-plus ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="plus" data-iconpos="notext" role="button">Add</a>
</div>
</div>
<div class="ui-field-contain edge-fastq-options" id="edge-r2g-aligner-sw">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Read Aligner<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-aligner1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Bowtie 2</label><input type="radio" name="edge-r2g-aligner" id="edge-r2g-aligner1" value="bowtie">
</div>
<div class="ui-radio ui-mini"><label for="edge-r2g-aligner2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active">BWA mem</label><input type="radio" name="edge-r2g-aligner" id="edge-r2g-aligner2" value="bwa"
checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-aligner3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Minimap2</label><input type="radio" name="edge-r2g-aligner" id="edge-r2g-aligner3" value="minimap2">
</div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Variant Call <a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-variantcall-tooltip" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-variantcall-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-r2g-variantcall-sw"
id="edge-r2g-variantcall-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-variantcall-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-r2g-variantcall-sw"
id="edge-r2g-variantcall-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Consensus Fasta <a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-getconsensus-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-r2g-getconsensus-sw"
id="edge-r2g-getconsensus-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-getconsensus-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-r2g-getconsensus-sw"
id="edge-r2g-getconsensus-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="edge-r2g-con-options edge-fastq-options" style="padding-left:0.8em">
<div class="ui-field-contain">
<label for="edge-r2g-con-min-cov"> Minimum Coverage<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-con-min-cov" id="edge-r2g-con-min-cov" data-mini="true" data-clear-btn="true"
value="5"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-r2g-con-alt-prop" id="edge-r2g-con-alt-prop-label"> Alternate Base
Threshold<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-r2g-con-alt-prop" id="edge-r2g-con-alt-prop" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.5" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini" aria-disabled="false">
<div class="ui-slider-bg ui-btn-active" style="width: 50%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.5" aria-valuetext="0.5" title="0.5" aria-labelledby="edge-r2g-con-alt-prop-label" style="left: 50%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-r2g-con-altIndel-prop" id="edge-r2g-con-altIndel-prop-label"> Indels
Threshold<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-r2g-con-altIndel-prop" id="edge-r2g-con-altIndel-prop" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.5" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini" aria-disabled="false">
<div class="ui-slider-bg ui-btn-active" style="width: 50%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.5" aria-valuetext="0.5" title="0.5" aria-labelledby="edge-r2g-con-altIndel-prop-label" style="left: 50%;"></a>
</div>
</div>
</div>
</div>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Lineage Assignment Mode<a href="#" id="edge-pangolinmode-tooltip" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a>
</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-con-pangolin-mode-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Usher</label><input type="radio" data-mini="true"
name="edge-r2g-con-pangolin-mode" id="edge-r2g-con-pangolin-mode-sw1" value="usher" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-con-pangolin-mode-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">PangoLearn</label><input type="radio" data-mini="true" name="edge-r2g-con-pangolin-mode"
id="edge-r2g-con-pangolin-mode-sw2" value="pangoLearn"></div>
</div>
</fieldset>
</div>
<div class="edge-right">|<a href="#" id="edge-r2g-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-r2g-options" class="edge-additional-options" style="display: none;">
<div class="edge-r2g-con-options edge-fastq-options edge-tool-parameters">
<p class="edge-center edge_tool_note">Consensus Generation Options</p>
<div class="ui-field-contain">
<label for="edge-r2g-con-min-mapQ">Minimum mapQ<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-con-min-mapQ" id="edge-r2g-con-min-mapQ" data-mini="true" data-clear-btn="true" value="60"
max="255"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-r2g-con-max-cov">Maximum Coverage<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-con-max-cov" id="edge-r2g-con-max-cov" data-mini="true" data-clear-btn="true"
value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-r2g-con-min-baseQ">Minimum baseQ<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-con-min-baseQ" id="edge-r2g-con-min-baseQ" data-mini="true" data-clear-btn="true" value="20"
max="41"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Disable BAQ<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-con-disableBAQ-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true"
name="edge-r2g-con-disableBAQ" id="edge-r2g-con-disableBAQ-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-con-disableBAQ-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-r2g-con-disableBAQ"
id="edge-r2g-con-disableBAQ-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Remove PCR Duplicates<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-con-pcrdedup-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-r2g-con-pcrdedup"
id="edge-r2g-con-pcrdedup-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-con-pcrdedup-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-r2g-con-pcrdedup"
id="edge-r2g-con-pcrdedup-sw2" value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Homopolymer Filter<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-con-homopolymer-filter-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true"
name="edge-r2g-con-homopolymer-filter" id="edge-r2g-con-homopolymer-filter-sw1" value="1"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-con-homopolymer-filter-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true"
name="edge-r2g-con-homopolymer-filter" id="edge-r2g-con-homopolymer-filter-sw2" value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>StrandBias Filter<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-con-strandbias-filter-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true"
name="edge-r2g-con-strandbias-filter" id="edge-r2g-con-strandbias-filter-sw1" value="1"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-con-strandbias-filter-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true"
name="edge-r2g-con-strandbias-filter" id="edge-r2g-con-strandbias-filter-sw2" value="0" checked="checked"></div>
</div>
</fieldset>
</div>
</div>
<div class="ui-field-contain edge-fastq-options">
<label for="edge-r2g-aligner-options">Aligner
Options<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn edge-aligner-options tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edge-r2g-aligner-options" id="edge-r2g-aligner-options" placeholder="(optional)"></div>
</div>
<div class="ui-field-contain edge-fastq-options">
<label for="edge-r2g-max-clip">MaxClip<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-max-clip" id="edge-r2g-max-clip" data-mini="true" data-clear-btn="true"
value="50"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<!--<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal">
<legend>Identify Unmapped Reads</legend>
<input type="radio" data-mini="true" name="edge-ref-unmapped-read-class" id="edge-ref-unmapped-read1" value="1">
<label for="edge-ref-unmapped-read1">Yes</label>
<input type="radio" data-mini="true" name="edge-ref-unmapped-read-class" id="edge-ref-unmapped-read2" value="0" checked="checked">
<label for="edge-ref-unmapped-read2">No</label>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal">
<legend>Identify Unmapped Contigs</legend>
<input type="radio" data-mini="true" name="edge-ref-unmapped-contig-class" id="edge-ref-unmapped-contig1" value="1">
<label for="edge-ref-unmapped-contig1">Yes</label>
<input type="radio" data-mini="true" name="edge-ref-unmapped-contig-class" id="edge-ref-unmapped-contig2" value="0" checked="checked">
<label for="edge-ref-unmapped-contig2">No</label>
</fieldset>
</div>
<p class="edge_tool_note">EDGE will try to classify reads and contigs that are unmapped to references by mapping them to NCBI RefSeq database.</p>-->
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Extract Mapped Reads</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-getmapped1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" name="edge-r2g-getmapped-sw" id="edge-r2g-getmapped1" value="1">
</div>
<div class="ui-radio ui-mini"><label for="edge-r2g-getmapped2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" name="edge-r2g-getmapped-sw" id="edge-r2g-getmapped2"
value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Extract Unmapped Reads</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-getunmapped1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" name="edge-r2g-getunmapped-sw" id="edge-r2g-getunmapped1"
value="1"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-getunmapped2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" name="edge-r2g-getunmapped-sw"
id="edge-r2g-getunmapped2" value="0" checked="checked"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-fastq-options">
<label for="edge-r2g-variantcall-min-qual">Variant QUAL<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="edge-r2g-variantcall-min-qual" id="edge-r2g-variantcall-min-qual" data-mini="true" data-clear-btn="true"
value="60"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Ploidy<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-r2g-variantcall-ploidy1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Haploid</label><input type="radio" name="edge-r2g-variantcall-ploidy"
id="edge-r2g-variantcall-ploidy1" value="haploid"></div>
<div class="ui-radio ui-mini"><label for="edge-r2g-variantcall-ploidy2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">Diploid</label><input type="radio" name="edge-r2g-variantcall-ploidy"
id="edge-r2g-variantcall-ploidy2" value="diploid" checked="checked"></div>
</div>
</fieldset>
</div>
</div>
</div>
</div>
<!-- Taxonomy classification -->
<div id="edge-runEDGE-tc" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed"
style="display: none;">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-taxa-sw" name="edge-taxa-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0">Off</option><option value="1" selected="TRUE">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 0%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 100%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0" aria-valuetext="Off" title="Off" aria-labelledby="edge-taxa-sw-label" style="left: 0%;"></a>
</div>
</div>
<label for="edge-taxa-sw" id="edge-taxa-sw-label">Taxonomy Classification</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<ol type="a">
<li class="edge-fastq-options">Read-based Taxonomy Classification</li>
<p class="edge_tool_note edge-fastq-options">EDGE will use all reads by default. You can change the behavior to use reads that are unmapped to the reference if Reference-based Analysis is on.</p>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Always Use All Reads</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-taxa-allreads1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-taxa-allreads"
id="edge-taxa-allreads1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-taxa-allreads2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-taxa-allreads" id="edge-taxa-allreads2"
value="0"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain edge-fastq-options" id="edge-taxa-tool-select">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Classification Tools<a href="#" class="tooltip ui-btn ui-alt-icon ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-reads-taxa-tooltip"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<label for="edge-taxa-enabled-tools" class="select">Run With Following Databases</label>
<div class="ui-select ui-mini">
<a href="#" role="button" id="edge-taxa-enabled-tools-button" aria-haspopup="true" class="ui-btn ui-icon-grid ui-btn-icon-right ui-corner-all ui-shadow ui-li-has-count ui-first-child ui-last-child"><span> GOTTCHA Genus, GOTTCHA Species , GOTTCHA Strain, GOTTCHA Genus, GOTTCHA Species, GOTTCHA Strain, Reads Mapping (BWA against RefSeq), MetaPhlAn2, Kraken2</span><span class="ui-li-count ui-body-inherit" style="">9</span></a><select
name="edge-taxa-enabled-tools" id="edge-taxa-enabled-tools" multiple="multiple" data-mini="true" data-native-menu="false" data-icon="grid" data-iconpos="right" tabindex="-1">
<option data-placeholder="true">Choose Classification Tools:</option>
<optgroup label="GOTTCHA Bacterial Databases">
<option value="gottcha-genDB-b" selected=""> GOTTCHA Genus</option>
<option value="gottcha-speDB-b" selected=""> GOTTCHA Species </option>
<option value="gottcha-strDB-b" selected=""> GOTTCHA Strain</option>
</optgroup>
<optgroup label="GOTTCHA Viral Databases">
<option value="gottcha-genDB-v" selected=""> GOTTCHA Genus</option>
<option value="gottcha-speDB-v" selected=""> GOTTCHA Species</option>
<option value="gottcha-strDB-v" selected=""> GOTTCHA Strain</option>
</optgroup>
<optgroup label="GOTTCHA2 BacteriaViruses Databases">
<option value="gottcha2-speDB-b"> GOTTCHA2 Species</option>
</optgroup>
<!--<optgroup label="GOTTCHA2 Viral Databases">
<option value="gottcha2-speDB-v" selected=""> GOTTCHA2 Species</option>
</optgroup>-->
<!--<optgroup label="PanGIA Databases">
<option value="pangia"> PanGIA NCBI Refseq89.mask_rrna </option>
</optgroup>-->
<optgroup label="Reads Mapping">
<option value="bwa" selected="">Reads Mapping (BWA against RefSeq)</option>
</optgroup>
<optgroup label="Other Tools">
<option value="metaphlan2" selected="">MetaPhlAn2</option>
<option value="kraken2" selected="">Kraken2</option>
<!--<option value="centrifuge" selected="">Centrifuge</option>-->
<!-- Adding DIAMOND -->
<option value="diamond">DIAMOND (Amino acid-based classification)</option>
</optgroup>
</select>
<div style="display: none;" id="edge-taxa-enabled-tools-listbox-placeholder"><!-- placeholder for edge-taxa-enabled-tools-listbox --></div>
</div>
</div>
</fieldset>
</div>
<div class="edge-right edge-fastq-options">|<a href="#" id="edge-taxa-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-taxa-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain edge-fastq-options">
<label for="edge-qc-q">Splitrim Quality Level<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" name="splitrim-minq" id="splitrim-minq" data-mini="true" data-clear-btn="true"
value="20"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain input-type-file edge-fastq-options">
<label for="edge-taxa-custom-db-tool" class="select">Custom DB Tool</label>
<div class="ui-select ui-mini" style="display: inline-flex; pointer-events: auto;">
<a href="#" role="button" id="edge-taxa-custom-db-tool-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span>Reads Mapping (BWA against custom DB)</span></a><select
name="edge-taxa-custom-db-tool" id="edge-taxa-custom-db-tool" data-mini="true" data-native-menu="false" tabindex="-1">
<option value="GOTTCHA-genDB-b"> GOTTCHA Bacteria Genus</option>
<option value="GOTTCHA-speDB-b"> GOTTCHA Bacteria Species </option>
<option value="GOTTCHA-strDB-b"> GOTTCHA Bacteria Strain</option>
<option value="GOTTCHA-genDB-v"> GOTTCHA Virus Genus</option>
<option value="GOTTCHA-speDB-v"> GOTTCHA Virus Species</option>
<option value="GOTTCHA-strDB-v"> GOTTCHA Virus Strain</option>
<!--
<option value="GOTTCHA2-genDB-v"> GOTTCHA2 Virus Genus</option>
<option value="GOTTCHA2-speDB-v"> GOTTCHA2 Virus Species</option>
<option value="GOTTCHA2-speDB-b"> GOTTCHA2 Bacteria Species </option>
<option value="pangia"> PanGIA database </option>
<option value="diamond"> DIAMOND database </option>
-->
<option value="BWA" selected="">Reads Mapping (BWA against custom DB)</option>
<option value="Metaphlan2">MetaPhlAn2</option>
<option value="Kraken">Kraken</option>
</select><a href="#" class="btnAdd-edge-taxa-custom-db ui-link ui-btn ui-icon-plus ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="plus" data-iconpos="notext" role="button">Add</a>
<div style="display: none; pointer-events: auto;" id="edge-taxa-custom-db-tool-listbox-placeholder"><!-- placeholder for edge-taxa-custom-db-tool-listbox --></div>
</div>
</div>
<div id="edge-taxa-custom-db-block1" class="edge-taxa-custom-db-block ui-field-contain input-type-file" style="display:none">
<label for="edge-taxa-custom-db-file-1">Custom Database</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: auto;"><input data-mini="true" name="edge-taxa-custom-db-file" id="edge-taxa-custom-db-file-1" type="text"
placeholder="absolute file path/select file"></div>
<div class="edge-file-selector" style="pointer-events: auto;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<li>Contig-based Taxonomy Classification</li>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Contigs Classification<a href="#" class="tooltip ui-btn ui-alt-icon ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-contig-taxa-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-contig-taxa-sw"
id="edge-contig-taxa-sw1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-contig-taxa-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-contig-taxa-sw"
id="edge-contig-taxa-sw2" value="0"></div>
</div>
</fieldset>
</div>
</ol>
</div>
</div>
<div id="edge-runEDGE-pa" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed"
style="display: none;">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-phylo-sw" name="edge-phylo-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0" selected="TRUE">Off</option><option value="1">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 0%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 100%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0" aria-valuetext="Off" title="Off" aria-labelledby="edge-phylo-sw-label" style="left: 0%;"></a>
</div>
</div>
<label for="edge-phylo-sw" id="edge-phylo-sw-label">Phylogenetic Analysis</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<p class="edge_tool_note">EDGE supports 5 pre-computed databases for SNP phylogeny analysis and two tree builders. FastTree is faster and RAxML is slower but more accurate.</p>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Tree Build Method</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-phylo-tree1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">FastTree</label><input type="radio" name="edge-phylo-tree" id="edge-phylo-tree1"
value="FastTree" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-phylo-tree2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">RAxML</label><input type="radio" name="edge-phylo-tree" id="edge-phylo-tree2" value="RAxML"
disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-phylo-patho">Pre-built SNP DB</label>
<div class="ui-select ui-mini" style="pointer-events: none;">
<div id="edge-phylo-patho-button" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow" style="pointer-events: none;"><span>Select a Pathogen...</span><select id="edge-phylo-patho" data-mini="true"
name="edge-phylo-patho" data-native-menu="true" disabled="">
<option value="">Select a Pathogen...</option>
<option value="Ecoli">Ecoli</option>
<option value="Yersinia">Yersinia</option>
<option value="Francisella">Francisella</option>
<option value="Brucella">Brucella</option>
<option value="Bacillus">Bacillus</option>
</select></div>
</div>
<!--<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal">
<legend>Specify Pathogen</legend>
<input type="radio" name="edge-phylo-patho" id="edge-phylo-patho1" value="Ecoli" check="checked">
<label for="edge-phylo-patho1">Ecoli</label>
<input type="radio" name="edge-phylo-patho" id="edge-phylo-patho2" value="Yersinia">
<label for="edge-phylo-patho2">Yersinia</label>
<input type="radio" name="edge-phylo-patho" id="edge-phylo-patho3" value="Francisella">
<label for="edge-phylo-patho3">Francisella</label>
<input type="radio" name="edge-phylo-patho" id="edge-phylo-patho4" value="Brucella">
<label for="edge-phylo-patho4">Brucella</label>
<input type="radio" name="edge-phylo-patho" id="edge-phylo-patho5" value="Bacillus">
<label for="edge-phylo-patho5">Bacillus</label>
</fieldset>-->
</div>
<p class="edge-center">or</p>
<p class="edge_tool_note">Select/Add Genomes or SRA Reads: The same species or at least within the same genus are recommended.</p>
<div class="ui-field-contain input-type-file">
<label for="edge-phylo-ref-select">Select Genome(s)<a href="#" class="tooltip ui-btn ui-alt-icon ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered"></a></label>
<div class="ui-select ui-mini" style="pointer-events: none;">
<a href="#" role="button" id="edge-phylo-ref-select-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow ui-li-has-count"><span>Search genomes...</span><span class="ui-li-count ui-body-inherit" style="display: none;">0</span></a><select
id="edge-phylo-ref-select" data-mini="true" name="edge-phylo-ref-select" data-native-menu="false" multiple="multiple" tabindex="-1" disabled="">
<option disabled="" data-placeholder="true">Search genomes...</option>
</select>
<div style="display: none; pointer-events: none;" id="edge-phylo-ref-select-listbox-placeholder"><!-- placeholder for edge-phylo-ref-select-listbox --></div>
</div>
</div>
<div id="edge-phylo-ref-select-ref-div" class="ui-field-contain input-type-file" style="display: none;">
<label for="edge-phylo-ref-select-ref">Select A Reference Genome from Selected Genomes</label>
<div class="ui-select ui-mini" style="pointer-events: none;">
<div id="edge-phylo-ref-select-ref-button" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow" style="pointer-events: none;"><span>Random</span><select id="edge-phylo-ref-select-ref" data-mini="true"
name="edge-phylo-ref-select-ref" data-native-menu="true" disabled="">
<option value="0" select="selected">Random</option>
</select></div>
</div>
</div>
<div id="edge-phylo-ref-file-block1" class="ui-field-contain input-type-file edge-phylo-ref-file-block">
<label for="edge-phylo-ref-file-1">Add Genome(s) </label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-phylo-ref-file[]" id="edge-phylo-ref-file-1"
placeholder="absolute FASTA file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
<a href="#" class="btnAdd-edge-phylo-ref-file ui-link ui-btn ui-icon-plus ui-btn-icon-notext ui-shadow ui-corner-all" data-role="button" data-icon="plus" data-iconpos="notext" role="button">Add</a>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-phylo-sra-acc"">SRA
Accessions<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-phylo-sra-acc-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-phylo-sra-acc" id="edge-phylo-sra-acc" placeholder="ex:SRR2133399,SRR576632" disabled=""></div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Bootstrap</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-phylo-bootstrap-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-phylo-bootstrap-sw"
id="edge-phylo-bootstrap-sw1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-phylo-bootstrap-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-phylo-bootstrap-sw"
id="edge-phylo-bootstrap-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain"><label for="edge-phylo-bootstrap-num">Bootstrap Number</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-phylo-bootstrap-num" id="edge-phylo-bootstrap-num" value="100"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div>
</div>
<div id="edge-runEDGE-gfa" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed"
style="display: none;">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-sg-sw" name="edge-sg-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0">Off</option><option value="1">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 0%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 100%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0" aria-valuetext="Off" title="Off" aria-labelledby="edge-sg-sw-label" style="left: 0%;"></a>
</div>
</div>
<label for="edge-sg-sw" id="edge-sg-sw-label">Gene Family Analysis</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<ol type="a">
<li class="edge-fastq-options">Read-based Gene Family Analysis</li>
<p class="edge_tool_note edge-fastq-options">EDGE will use <a href="http://huttenhower.sph.harvard.edu/shortbred" target="_blank" class="ui-link">ShortBRED</a> to search the reads for Antibiotic Resistance genes from
<a href="http://ardb.cbcb.umd.edu/" target="_blank" class="ui-link">ARDB</a> and <a href="http://www.dantaslab.org/resfams/" target="_blank" class="ui-link">Resfams</a> and for Virulence genes from
<a href="http://www.mgc.ac.cn/VFs/main.htm" target="_blank" class="ui-link">VFDB.</a></p>
<div class="ui-field-contain edge-fastq-options">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Reads Gene Family Analysis</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-reads-sg-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-reads-sg-sw"
id="edge-reads-sg-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-reads-sg-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-reads-sg-sw" id="edge-reads-sg-sw2"
value="0" disabled=""></div>
</div>
</fieldset>
</div>
<li>Contig-based (CDS) Gene Family Analysis</li>
<p class="edge_tool_note">EDGE will use <a href="http://huttenhower.sph.harvard.edu/shortbred" target="_blank" class="ui-link">ShortBRED</a> to search the CDSs on the contigs for Virulence genes from
<a href="http://www.mgc.ac.cn/VFs/main.htm" target="_blank" class="ui-link">VFDB.</a></p>
<p class="edge_tool_note">EDGE will use <a href="https://card.mcmaster.ca/analyze/rgi" target="_blank" class="ui-link">RGI (Resistance Gene Identifier)</a> to search the CDSs on the contigs for Antibiotic Resistance genes from
<a href="https://card.mcmaster.ca" target="_blank" class="ui-link">CARD</a>.</p>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>CDS Gene Family Analysis</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-orfs-sg-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-orfs-sg-sw"
id="edge-orfs-sg-sw1" value="1" checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-orfs-sg-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-orfs-sg-sw" id="edge-orfs-sg-sw2" value="0"
disabled=""></div>
</div>
</fieldset>
</div>
</ol>
<div class="edge-right">|<a href="#" id="edge-sg-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-sg-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain">
<label for="edge-sg-identity-options" class="edge-identity-options">ShortBRED Minimum Percent Identity</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="number" data-mini="true" data-clear-btn="false" name="edge-sg-identity-options" id="edge-sg-identity-options" value="95" disabled=""></div>
</div>
<div class="ui-field-contain">
<label for="edge-sg-length-options" class="edge-length-options">ShortBRED Minimum Percent Length</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="number" data-mini="true" data-clear-btn="false" name="edge-sg-length-options" id="edge-sg-length-options" value="95" disabled=""></div>
</div>
</div>
</div>
</div>
<div id="edge-runEDGE-ppa" data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content ui-collapsible-collapsed"
style="display: none;">
<h4 class="ui-collapsible-heading ui-collapsible-heading-collapsed"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
</a>
<div class="ui-field-contain edge-collapsible-options"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit">
<select id="edge-primer-sw" name="edge-primer-sw" data-role="slider" data-mini="true" tabindex="-1" class="ui-slider-switch">
<option value="0">Off</option><option value="1">On</option>
</select></a>
<div role="application" class="ui-slider ui-slider-switch ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"><span class="ui-slider-label ui-slider-label-a ui-btn-active" role="img" style="width: 0%;">On</span><span class="ui-slider-label ui-slider-label-b" role="img" style="width: 100%;">Off</span></a>
<div class="ui-slider-inneroffset">
<a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-d ui-btn-icon-left ui-btn-inherit"></a><a href="#" class="ui-slider-handle ui-slider-handle-snapping ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0" aria-valuetext="Off" title="Off" aria-labelledby="edge-primer-sw-label" style="left: 0%;"></a>
</div>
</div>
<label for="edge-primer-sw" id="edge-primer-sw-label">PCR Primer Analysis</label>
</div>
<span class="ui-collapsible-heading-status"> click to expand contents</span>
</h4>
<div class="ui-collapsible-content ui-body-inherit ui-collapsible-content-collapsed" aria-hidden="true">
<div class="edge-tabs">
<div class="ui-grid-a">
<div class="ui-block-a"><a href="#" data-id="edge-primer-valid-parameters" class="ui-btn ui-mini ui-btn-active"> a. Primer Validation</a></div>
<div class="ui-block-b"><a href="#" data-id="edge-primer-design-parameters" class="ui-btn ui-mini">b. Primer Design</a></div>
</div>
</div>
<div id="edge-primer-valid-parameters">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Run Primer Validation</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-primer-valid-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-primer-valid-sw"
id="edge-primer-valid-sw1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-primer-valid-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-primer-valid-sw"
id="edge-primer-valid-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<p class="edge_tool_note">Given a primer file, EDGE will run validation of the primer pair to the reference and/or assembled contigs, as available.</p>
<div class="ui-field-contain input-type-file">
<label for="edge-primer-valid-file">Primer Fasta Sequences</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset" style="pointer-events: none;"><input type="text" data-mini="true" name="edge-primer-valid-file" id="edge-primer-valid-file"
placeholder="absolute file path/select file" disabled=""></div>
<div class="edge-file-selector" style="pointer-events: none;">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Maximum Mismatch</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-primer-valid-mm0" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">0</label><input type="radio" name="edge-primer-valid-mm" id="edge-primer-valid-mm0" value="0"
disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-primer-valid-mm1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active">1</label><input type="radio" name="edge-primer-valid-mm" id="edge-primer-valid-mm1" value="1"
checked="checked" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-primer-valid-mm2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">2</label><input type="radio" name="edge-primer-valid-mm" id="edge-primer-valid-mm2" value="2" disabled="">
</div>
<div class="ui-radio ui-mini"><label for="edge-primer-valid-mm3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">3</label><input type="radio" name="edge-primer-valid-mm" id="edge-primer-valid-mm3" value="3" disabled="">
</div>
<div class="ui-radio ui-mini"><label for="edge-primer-valid-mm4" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">4</label><input type="radio" name="edge-primer-valid-mm" id="edge-primer-valid-mm4" value="4"
disabled=""></div>
</div>
</fieldset>
</div>
</div> <!-- edge-primer-valid-parameters -->
<div id="edge-primer-design-parameters" style="display: none;">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Run Primer Design</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-primer-adj-sw1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-primer-adj-sw"
id="edge-primer-adj-sw1" value="1" disabled=""></div>
<div class="ui-radio ui-mini"><label for="edge-primer-adj-sw2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-last-child">No</label><input type="radio" data-mini="true" name="edge-primer-adj-sw"
id="edge-primer-adj-sw2" value="0" checked="checked" disabled=""></div>
</div>
</fieldset>
</div>
<p class="edge_tool_note">EDGE will design primers based on the assembled contigs.</p>
<div class="ui-field-contain">
<label for="edge-primer-adj-tm-opt">Tm Optimum (C)</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-primer-adj-tm-opt" id="edge-primer-adj-tm-opt" value="59"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-primer-adj-tm-min" id="edge-primer-adj-tm-min-label">Tm Range (C)</label>
<div data-role="rangeslider" data-mini="true" class="ui-rangeslider ui-mini">
<input type="number" data-type="range" name="edge-primer-adj-tm-min" id="edge-primer-adj-tm-min" min="40" max="80" value="57"
class="ui-shadow-inset ui-corner-all ui-slider-input ui-rangeslider-first ui-body-inherit mobile-slider-disabled" disabled="">
<input type="number" data-type="range" name="edge-primer-adj-tm-max" id="edge-primer-adj-tm-max" min="40" max="80" value="63"
class="ui-shadow-inset ui-corner-all ui-slider-input ui-rangeslider-last ui-body-inherit mobile-slider-disabled" disabled="">
<div class="ui-rangeslider-sliders">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini ui-state-disabled" aria-disabled="true">
<div class="ui-slider-bg ui-btn-active" style="width: 15%; margin-left: 42%;"></div>
</div>
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini ui-state-disabled" aria-disabled="true">
<div class="ui-slider-bg ui-btn-active" style="width: 15%; margin-left: 42%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow ui-btn-null" role="slider" aria-valuemin="40" aria-valuemax="80" aria-valuenow="57" aria-valuetext="57" title="57" aria-labelledby="edge-primer-adj-tm-min-label" style="left: 42.5%;"></a><a href="#" class="ui-slider-handle ui-btn ui-shadow ui-btn-null" role="slider" aria-valuemin="40" aria-valuemax="80" aria-valuenow="63" aria-valuetext="63" title="63" aria-labelledby="edge-primer-adj-tm-max-label" style="left: 57.5%;"></a>
</div>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-primer-adj-len-opt">Length Optimum (bp)</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-primer-adj-len-opt" id="edge-primer-adj-len-opt" min="10"
max="40" value="20" disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-primer-adj-len-min" id="edge-primer-adj-len-min-label">Length Range (bp)</label>
<div data-role="rangeslider" data-mini="true" class="ui-rangeslider ui-mini">
<input type="number" data-type="range" name="edge-primer-adj-len-min" id="edge-primer-adj-len-min" min="10" max="40" value="18"
class="ui-shadow-inset ui-corner-all ui-slider-input ui-rangeslider-first ui-body-inherit mobile-slider-disabled" disabled="">
<input type="number" data-type="range" name="edge-primer-adj-len-max" id="edge-primer-adj-len-max" min="10" max="40" value="27"
class="ui-shadow-inset ui-corner-all ui-slider-input ui-rangeslider-last ui-body-inherit mobile-slider-disabled" disabled="">
<div class="ui-rangeslider-sliders">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini ui-state-disabled" aria-disabled="true">
<div class="ui-slider-bg ui-btn-active" style="width: 30%; margin-left: 26%;"></div>
</div>
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini ui-state-disabled" aria-disabled="true">
<div class="ui-slider-bg ui-btn-active" style="width: 30%; margin-left: 26%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow ui-btn-null" role="slider" aria-valuemin="10" aria-valuemax="40" aria-valuenow="18" aria-valuetext="18" title="18" aria-labelledby="edge-primer-adj-len-min-label" style="left: 26.6667%;"></a><a href="#" class="ui-slider-handle ui-btn ui-shadow ui-btn-null" role="slider" aria-valuemin="10" aria-valuemax="40" aria-valuenow="27" aria-valuetext="27" title="27" aria-labelledby="edge-primer-adj-len-max-label" style="left: 56.6667%;"></a>
</div>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-primer-adj-df">Background Tm Differential (C)</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-primer-adj-df" id="edge-primer-adj-df" min="0" max="10" value="5"
disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<label for="edge-primer-adj-num">Number of Primer Pairs</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-primer-adj-num" id="edge-primer-adj-num" min="1" max="10"
value="5" disabled=""><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
</div> <!-- edge-primer-design-parameters -->
</div>
</div>
</div> <!--Choose Proceses collapsible for edge-main-pipeline-input"-->
<div class="edge-qiime-pipeline-input" style="display: none;">
<div data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" data-collapsed="false" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content">
<h4 class="ui-collapsible-heading"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-u ui-btn-icon-left ui-btn-inherit">Parameters<span class="ui-collapsible-heading-status"> click to collapse contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit" aria-hidden="false">
<ol type="a">
<li>Barcode Options</li>
<div id="edge-qiime-barcode-fq-file-block1" class="ui-field-contain input-type-file edge-qiime-barcode-fq-file-block">
<label for="edge-qiime-barcode-fq-file-input-1">Barcode Fastq
File<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-qiime-barcode-fq-file-tooltip" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input data-mini="true" type="text" name="edge-qiime-barcode-fq-file-input[]" id="edge-qiime-barcode-fq-file-input-1"
placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<li>Reads Quality Control and Feature Table Construction</li>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Quality Offset<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qiime-phred-offset1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Phred+33</label><input type="radio" data-mini="true"
name="edge-qiime-phred-offset" id="edge-qiime-phred-offset1" value="33" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-phred-offset2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Phred+64</label><input type="radio" data-mini="true" name="edge-qiime-phred-offset"
id="edge-qiime-phred-offset2" value="64"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Quality Control Method<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-qiime-qcm-tooltip" style="display: none;"></a>
</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qiime-qcMethod1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">DADA2</label><input type="radio" data-mini="true" name="edge-qiime-qcMethod"
id="edge-qiime-qcMethod1" value="dada2" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-qcMethod2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Deblur</label><input type="radio" data-mini="true" name="edge-qiime-qcMethod"
id="edge-qiime-qcMethod2" value="deblur"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain dada2-options">
<label for="edge-qiime-trimLeftForward">Trim 5'end Forward<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-trimLeftForward" id="edge-qiime-trimLeftForward" min="0"
max="150" value="20"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain dada2-options">
<label for="edge-qiime-trimLeftReverse">Trim 5'end Reverse<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-trimLeftReverse" id="edge-qiime-trimLeftReverse" min="0"
max="150" value="20"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain dada2-options">
<label for="edge-qiime-truncLenForward">Truncation Len Forward<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-truncLenForward" id="edge-qiime-truncLenForward" min="0"
max="300" value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain dada2-options">
<label for="edge-qiime-truncLenReverse">Truncation Len Reverse<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-truncLenReverse" id="edge-qiime-truncLenReverse" min="0"
max="300" value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain dada2-options">
<label for="edge-qiime-trimLen">SE Trim Length<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-trimLen" id="edge-qiime-trimLen" min="0" max="150"
value="20"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain deblur-options" style="display: none;">
<label for="edge-qiime-phred-quality-threshold">PHRED Quality<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-phred-quality-threshold"
id="edge-qiime-phred-quality-threshold" min="1" max="40" value="4"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain deblur-options" style="display: none;">
<label for="edge-qiime-max-n">Max "N" base<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-max-n" id="edge-qiime-max-n" min="0" max="100"
value="1"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain deblur-options" style="display: none;">
<label for="edge-qiime-min-per-read-length-fraction" id="edge-qiime-min-per-read-length-fraction-label">Min Per Read Length
Fraction<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-qiime-min-per-read-length-fraction" id="edge-qiime-min-per-read-length-fraction" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.5"
step=".01" class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 50%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.5" aria-valuetext="0.5" title="0.5" aria-labelledby="edge-qiime-min-per-read-length-fraction-label" style="left: 50%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain dada2-options deblur-options" style="display: none;">
<label for="edge-qiime-trunLen">SE Truncation Len<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-trunLen" id="edge-qiime-trunLen" min="0" max="350"
value="0"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<li>Sampling</li>
<div class="ui-field-contain">
<label for="edge-qiime-sampling-depth">Sampling Depth<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-qiime-sampling-depth" id="edge-qiime-ampling-depth" min="100"
max="50000" value="1000"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Auto-Adjust Sampling Depth<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-qiime-autoDepth1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" data-mini="true" name="edge-qiime-autoDepth"
id="edge-qiime-autoDepth1" value="1" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-qiime-autoDepth2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" data-mini="true" name="edge-qiime-autoDepth"
id="edge-qiime-autoDepth2" value="0"></div>
</div>
</fieldset>
</div>
</ol>
</div>
</div>
</div><!-- edge-qiime-pipeline parameters -->
<div class="edge-targetedngs-pipeline-input" style="display: none;">
<div data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" data-collapsed="false" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content">
<h4 class="ui-collapsible-heading"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-u ui-btn-icon-left ui-btn-inherit">Parameters<span class="ui-collapsible-heading-status"> click to collapse contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit" aria-hidden="false">
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Platform</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-targetedngs-platform1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Illumina</label><input type="radio" data-mini="true"
name="edge-targetedngs-platform" id="edge-targetedngs-platform1" value="illumina" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-targetedngs-platform2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Nanopore</label><input type="radio" data-mini="true" name="edge-targetedngs-platform"
id="edge-targetedngs-platform2" value="ont2d"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Mode</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-targetedngs-mode1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Paired-End</label><input type="radio" data-mini="true" name="edge-targetedngs-mode"
id="edge-targetedngs-mode1" value="PE" checked="checked"></div>
<div class="ui-radio ui-mini"><label for="edge-targetedngs-mode2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Single-End</label><input type="radio" data-mini="true" name="edge-targetedngs-mode"
id="edge-targetedngs-mode2" value="SE"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-q-cutoff" id="edge-targetedngs-q-cutoff-label">Quality Calculation
Cutoff<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-q-cutoff" id="edge-targetedngs-q-cutoff" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.8145" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 81.45%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.81" aria-valuetext="0.81" title="0.81" aria-labelledby="edge-targetedngs-q-cutoff-label" style="left: 81.45%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-depth-cutoff">Depth Filter<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-targetedngs-depth-cutoff" id="edge-targetedngs-depth-cutoff"
min="100" max="50000" value="1000"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<div class="edge-right">|<a href="#" id="edge-targetedngs-toggle" class="edge-additional-options-toggle ui-link"> additional options </a>|</div>
<div id="edge-targetedngs-options" class="edge-additional-options" style="display: none;">
<div class="ui-field-contain">
<label for="edge-targetedngs-len-cutoff">Read Length Filter<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset ui-input-has-clear"><input type="number" data-mini="true" data-clear-btn="true" name="edge-targetedngs-len-cutoff" id="edge-targetedngs-len-cutoff" min="1"
max="500" value="100"><a href="#" class="ui-input-clear ui-btn ui-icon-delete ui-btn-icon-notext ui-corner-all" title="Clear text">Clear text</a></div>
</div>
<p class="edge_tool_note">The following parameters will affect how the Quality Calcuation derived. The four weight parameters should sum up to 1. Mouse over the label to see the notes.</p>
<div class="ui-field-contain">
<label for="edge-targetedngs-ec" id="edge-targetedngs-ec-label">Expected
Coverage<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-ec" id="edge-targetedngs-ec" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="1" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 100%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="1" aria-valuetext="1" title="1" aria-labelledby="edge-targetedngs-ec-label" style="left: 100%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-eid" id="edge-targetedngs-eid-label">Expected
Identity<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-eid" id="edge-targetedngs-eid" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="1" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 100%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="1" aria-valuetext="1" title="1" aria-labelledby="edge-targetedngs-eid-label" style="left: 100%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-ebq" id="edge-targetedngs-ebq-label">Expected
BaseQ<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-ebq" id="edge-targetedngs-ebq" data-mini="true" data-highlight="true" min="1" max="41" value="37" step="1"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 90%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="1" aria-valuemax="41" aria-valuenow="37" aria-valuetext="37" title="37" aria-labelledby="edge-targetedngs-ebq-label" style="left: 90%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-emq" id="edge-targetedngs-emq-label">Expected Mapping
Quality<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-emq" id="edge-targetedngs-emq" data-mini="true" data-highlight="true" min="0" max="255" value="60" step="1"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 23.5294%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="255" aria-valuenow="60" aria-valuetext="60" title="60" aria-labelledby="edge-targetedngs-emq-label" style="left: 23.5294%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-cw" id="edge-targetedngs-cw-label">Coverage Weight</label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-cw" id="edge-targetedngs-cw" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.25" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 25%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.25" aria-valuetext="0.25" title="0.25" aria-labelledby="edge-targetedngs-cw-label" style="left: 25%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-iw" id="edge-targetedngs-iw-label">Identity Weight</label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-iw" id="edge-targetedngs-iw" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.25" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 25%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.25" aria-valuetext="0.25" title="0.25" aria-labelledby="edge-targetedngs-iw-label" style="left: 25%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-bw" id="edge-targetedngs-bw-label">BaseQ Weight</label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-bw" id="edge-targetedngs-bw" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.25" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 25%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.25" aria-valuetext="0.25" title="0.25" aria-labelledby="edge-targetedngs-bw-label" style="left: 25%;"></a>
</div>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-targetedngs-mw" id="edge-targetedngs-mw-label">MapQ Weight</label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-targetedngs-mw" id="edge-targetedngs-mw" data-mini="true" data-highlight="true" min="0.0" max="1.0" value="0.25" step=".01"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 25%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0" aria-valuemax="1" aria-valuenow="0.25" aria-valuetext="0.25" title="0.25" aria-labelledby="edge-targetedngs-mw-label" style="left: 25%;"></a>
</div>
</div>
</div>
</div>
</div>
</div>
</div><!--edge-targetedngs-pipeline parameters-->
<div class="edge-piret-pipeline-input" style="display: none;">
<div data-role="collapsible" data-collapsed-icon="carat-d" data-expanded-icon="carat-u" data-collapsed="false" class="ui-collapsible ui-collapsible-inset ui-corner-all ui-collapsible-themed-content">
<h4 class="ui-collapsible-heading"><a href="#" class="ui-collapsible-heading-toggle ui-btn ui-icon-carat-u ui-btn-icon-left ui-btn-inherit">Parameters<span class="ui-collapsible-heading-status"> click to collapse contents</span></a></h4>
<div class="ui-collapsible-content ui-body-inherit" aria-hidden="false">
<ol type="a">
<li>Required arguments</li>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Kingdom</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-piret-kingdom1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Prokarya</label><input type="radio" data-mini="true" name="edge-piret-kingdom"
id="edge-piret-kingdom1" value="prokarya" checked=""></div>
<div class="ui-radio ui-mini"><label for="edge-piret-kingdom2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Eukarya</label><input type="radio" data-mini="true" name="edge-piret-kingdom" id="edge-piret-kingdom2"
value="eukarya"></div>
<div class="ui-radio ui-mini"><label for="edge-piret-kingdom3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Both</label><input type="radio" data-mini="true" name="edge-piret-kingdom"
id="edge-piret-kingdom3" value="both"></div>
</div>
</fieldset>
</div>
<div id="edge-piret-prok-input">
<div class="ui-field-contain input-type-file">
<label for="edge-piret-prok-fasta-file">Prokaryotic Reference Fasta</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-piret-prok-fasta-file" id="edge-piret-prok-fasta-file" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-piret-prok-gff-file">Prokaryotic Reference GFF</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-piret-prok-gff-file" id="edge-piret-prok-gff-file" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<div id="edge-piret-euk-input" style="display: none;">
<div class="ui-field-contain input-type-file">
<label for="edge-piret-euk-fasta-file">Eukaryotic Reference Fasta</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-piret-euk-fasta-file" id="edge-piret-euk-fasta-file" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-piret-euk-gff-file">Eukaryotic Reference GFF</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-piret-euk-gff-file" id="edge-piret-euk-gff-file" placeholder="absolute file path/select file"></div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
</div>
<li>Optional arguments</li>
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Strandedness</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edge-piret-stranded1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Not Stranded</label><input type="radio" data-mini="true" name="edge-piret-stranded"
id="edge-piret-stranded1" value="0" checked=""></div>
<div class="ui-radio ui-mini"><label for="edge-piret-stranded2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off">Forward</label><input type="radio" data-mini="true" name="edge-piret-stranded" id="edge-piret-stranded2"
value="1"></div>
<div class="ui-radio ui-mini"><label for="edge-piret-stranded3" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">Reverse</label><input type="radio" data-mini="true" name="edge-piret-stranded"
id="edge-piret-stranded3" value="2"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain">
<label for="edge-piret-method">Method<a href="#" class="tooltip ui-btn ui-corner-all ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" id="edge-piret-method-l" style="display: none;"></a></label>
<div class="ui-select ui-mini"><a href="#" role="button" id="edge-piret-method-button" aria-haspopup="true" class="ui-btn ui-icon-carat-d ui-btn-icon-right ui-corner-all ui-shadow"><span>edgeR</span></a><select id="edge-piret-method"
data-mini="true" name="edge-piret-method" data-native-menu="false" tabindex="-1">
<option value="edgeR">edgeR</option>
<option value="DESeq2">DESeq2</option>
<option value="ballgown" disabled="">ballgown</option>
<option value="DEedge">DEedge</option>
<option value="balledgeR" disabled="">balledgeR</option>
<option value="DEgown" disabled="">DEgown</option>
<!--<option value="all">all</option>-->
</select>
<div style="display: none;" id="edge-piret-method-listbox-placeholder"><!-- placeholder for edge-piret-method-listbox --></div>
</div>
</div>
<div class="ui-field-contain input-type-file">
<label for="edge-piret-hisat2-index-file">HISAT2 index file</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" name="edge-piret-hisat2-index-file" id="edge-piret-hisat2-index-file" placeholder="absolute file path/select file">
</div>
<div class="edge-file-selector">
<a href="#edge_file_dialog" aria-haspopup="true" data-rel="popup" data-position-to="window" data-transition="pop" data-mini="true" class="ui-btn ui-shadow ui-corner-all ui-icon-bullets ui-btn-icon-notext" aria-owns="edge_file_dialog" aria-expanded="false">file</a>
</div>
</div>
<div class="ui-field-contain">
<label for="edge-piret-pvaule">Q-value<a href="#" class="tooltip ui-btn ui-nodisc-icon ui-corner-all ui-btn-inline ui-icon-info ui-btn-icon-notext my-tooltip-btn tooltipstered" style="display: none;"></a></label>
<div class="ui-slider ui-mini"><input type="number" data-type="range" name="edge-piret-pvalue" id="edge-piret-pvalue" data-mini="true" data-highlight="true" min="0.001" max="0.5" value="0.001" step=".001"
class="ui-shadow-inset ui-body-inherit ui-corner-all ui-mini ui-slider-input">
<div role="application" class="ui-slider-track ui-shadow-inset ui-bar-inherit ui-corner-all ui-mini">
<div class="ui-slider-bg ui-btn-active" style="width: 0%;"></div>
<a href="#" class="ui-slider-handle ui-btn ui-shadow" role="slider" aria-valuemin="0.001" aria-valuemax="0.5" aria-valuenow="0.001" aria-valuetext="0.001" title="0.001" aria-labelledby="edge-piret-pvalue-label" style="left: 0%;"></a>
</div>
</div>
</div>
</ol>
</div>
</div>
</div><!--edge-piret-pipeline parameters-->
<div class="edge-center">
<div class="ui-btn ui-input-btn ui-corner-all ui-shadow ui-btn-inline ui-mini">Submit<input data-mini="true" type="button" id="edge-form-submit" data-inline="true" class="edge-center" value="Submit"></div>
<div class="ui-btn ui-input-btn ui-corner-all ui-shadow ui-btn-inline ui-mini">Reset<input data-mini="true" type="button" id="edge-form-reset" data-inline="true" class="edge-center" value="Reset"></div>
<div class="ui-btn ui-input-btn ui-corner-all ui-shadow ui-btn-inline ui-mini" style="display: none;">Save modified parameters<input data-mini="true" type="button" id="edge-form-reconfig-rerun" data-inline="true" class="edge-center"
value="Save modified parameters"></div>
</div>
<ul data-role="listview" data-inset="true" id="edge-submit-info" class="ui-listview ui-listview-inset ui-corner-all ui-shadow">
<!-- <li data-role="list-divider">Information</li> -->
</ul>
</div><!-- /content -->
<div style="display: none;" id="edge_integrity_dialog-placeholder"><!-- placeholder for edge_integrity_dialog --></div><!-- /integrity check dialog -->
<div style="display: none;" id="edge_file_dialog-placeholder"><!-- placeholder for edge_file_dialog --></div><!-- /file viewer -->
<div style="display: none;" id="edge_confirm_dialog-placeholder"><!-- placeholder for edge_confirm_dialog --></div><!-- /proceed action -->
<div style="display: none;" id="edge_log_dialog-placeholder"><!-- placeholder for edge_log_dialog --></div><!-- /log viewer -->
<!-- User Management -->
<div style="display: none;" id="popupUser-placeholder"><!-- placeholder for popupUser --></div>
<div style="display: none;" id="signInForm-placeholder"><!-- placeholder for signInForm --></div> <!-- SignIn dialog -->
<div style="display: none;" id="signUpForm-placeholder"><!-- placeholder for signUpForm --></div> <!-- signUpForm dialog -->
<div style="display: none;" id="myuplodsfileList-placeholder"><!-- placeholder for myuplodsfileList --></div>
<div style="display: none;" id="UpdateSysPropertyForm-placeholder"><!-- placeholder for UpdateSysPropertyForm --></div> <!-- UpdateSysProperty dialog -->
<div style="display: none;" id="UpdateProfileForm-placeholder"><!-- placeholder for UpdateProfileForm --></div> <!-- updateProfile dialog -->
</form><form id="edge-uploadfile-form" data-ajax="false" enctype="multipart/form-data">
<div role="main" id="edge-content-uploadfile" class="ui-content edge-content edge-main-page" style="display: none;">
<h2>Upload files</h2>
<p class="edge_tool_note">Max file size is <span id="edge-upload-maxFileSize">1gb</span> and total user space up to <span id="edge-upload-maxFileTotalSize">1</span>gb. Allowed File types are fastq, fasta, genbank, gff, xlsx and text
(txt,bed,config,ini) and can be in gzip format. Files will be kept for <span id="edge-upload-expiration-days">180</span> days.</p>
<div id="uploader">
<p>You are not logged in or your browser doesn't have Flash, Silverlight or HTML5 support.</p>
</div>
<span id="docker-file-transfer" class="ui-content edge-content" style="display: none;">
<h2>Alternative uploading methods</h2>
<p class="edge_tool_note">
</p>
<div id="edge-uploadfile-notice"> Web uploader is designed to upload small files. When the sizes of uploading files are <strong>>1000MB</strong>, please use one of following options: <ul>
<li>Directly copy files to user's MyUploads directory from the host OS (mounted EDGE_input directory while docker run): <ul>- The path is: <div class="edge-uploadfile-myuploads-path">/path/to/EDGE_input/<span
class="edge-uploadfile-scp-path"></span>/MyUploads/</div>
</ul>
<ul>- For example: <div class="edge-uploadfile-myuploads-path">cp /path/to/your_seq.fastq /path/to/EDGE_input/<span class="edge-uploadfile-scp-path"></span>/MyUploads/</div>
</ul>
</li>
</ul>
</div>
<p></p>
</span>
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
</div> <!-- uploadfile-form -->
</form><form id="edgesite-form">
<div role="main" id="edgesite-content" class="ui-content edge-content edge-main-page" style="display: none;">
<h2>EdgeSite</h2>
<p class="edge_tool_note">Please fill out this form before using 'Run EDGE'.</p>
<div class="ui-field-contain">
<label for="edgesite-org">Organization Full Name</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edgesite-org" id="edgesite-org" maxlength="30" placeholder="Your organization full name"></div>
</div>
<div class="ui-field-contain">
<label for="edgesite-acronym">Acronym</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input type="text" data-mini="true" data-clear-btn="false" name="edgesite-acronym" id="edgesite-acronym" maxlength="30" placeholder="Your organization acronym">
</div>
</div>
<!-- geo autocomplete -->
<div id="edgesite-geo">
<div class="ui-field-contain">
<label>Location</label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-shadow-inset"><input name="edgesite-location" id="edgesite-geocomplete" type="text" placeholder="Type in an address to let system auto fill the location fields below"></div>
</div>
<div class="ui-field-contain">
<label></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input name="locality" id="edgesite-city" data-mini="true" data-clear-btn="false" type="text" placeholder="City"></div>
</div>
<div class="ui-field-contain">
<label></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input name="administrative_area_level_1" id="edgesite-state" data-mini="true" data-clear-btn="false" type="text" placeholder="State"></div>
</div>
<div class="ui-field-contain">
<label></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input name="country" id="edgesite-country" data-mini="true" data-clear-btn="false" type="text" placeholder="Country"></div>
</div>
<div class="ui-field-contain">
<label></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input name="lat" id="edgesite-lat" data-mini="true" data-clear-btn="false" type="text" placeholder="Latitude"></div>
</div>
<div class="ui-field-contain">
<label></label>
<div class="ui-input-text ui-body-inherit ui-corner-all ui-mini ui-shadow-inset"><input name="lng" id="edgesite-lng" data-mini="true" data-clear-btn="false" type="text" placeholder="Longitude"></div>
</div>
</div>
<!-- end geo -->
<div class="ui-field-contain">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Enable Sample Metadata? <a href="#" class="tooltip my-tooltip-btn ui-btn ui-alt-icon ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext tooltipstered"></a>
</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edgesite-enable-metadata1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" name="edgesite-enable-metadata"
id="edgesite-enable-metadata1" value="yes" checked=""></div>
<div class="ui-radio ui-mini"><label for="edgesite-enable-metadata2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" name="edgesite-enable-metadata" id="edgesite-enable-metadata2"
value="no"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain" id="edgesite-share-metadata-div">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
<div role="heading" class="ui-controlgroup-label">
<legend>Share Sample Metadata/Pathogens with BSVE? <a href="#" class="tooltip my-tooltip-btn ui-btn ui-alt-icon ui-nodisc-icon ui-btn-inline ui-icon-info ui-btn-icon-notext tooltipstered"></a>
</legend>
</div>
<div class="ui-controlgroup-controls ">
<div class="ui-radio ui-mini"><label for="edgesite-share-metadata1" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-on ui-btn-active ui-first-child">Yes</label><input type="radio" name="edgesite-share-metadata"
id="edgesite-share-metadata1" value="yes" checked=""></div>
<div class="ui-radio ui-mini"><label for="edgesite-share-metadata2" class="ui-btn ui-corner-all ui-btn-inherit ui-radio-off ui-last-child">No</label><input type="radio" name="edgesite-share-metadata" id="edgesite-share-metadata2"
value="no"></div>
</div>
</fieldset>
</div>
<div class="ui-field-contain" id="edgesite-autoshare-metadata-div">
<fieldset data-role="controlgroup" data-mini="true" data-type="horizontal" class="ui-controlgroup ui-controlgroup-horizontal ui-corner-all ui-mini">
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* 2021-12-08 21:44:00
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ACTIV_ERR4969389
* 2021-10-31 22:08:49
ACTIV_ERR4969386
* 2021-10-31 22:08:49
ACTIV_ERR4969356
* 2021-10-31 22:08:49
ACTIV_ERR4969351
* 2021-10-31 22:08:49
ACTIV_ERR4969348
* 2021-10-31 22:08:49
ACTIV_ERR4969328
* 2021-10-31 22:08:49
ACTIV_ERR4969137
* 2021-10-31 22:08:49
ACTIV_ERR4969052
* 2021-10-31 22:08:49
ACTIV_ERR4969051
* 2021-10-31 22:08:49
ACTIV_ERR4969042
* 2021-10-31 22:08:49
ACTIV_ERR4969036
* 2021-10-31 22:08:49
ACTIV_ERR4969193
* 2021-10-31 22:08:49
ACTIV_ERR4969184
* 2021-10-31 22:08:49
ACTIV_ERR4969181
* 2021-10-31 22:08:49
ACTIV_ERR4969180
* 2021-10-31 22:08:48
ACTIV_ERR4969135
* 2021-10-31 22:08:48
ACTIV_ERR4969134
* 2021-10-31 22:08:48
ACTIV_ERR4969050
* 2021-10-31 22:08:48
ACTIV_ERR4969044
* 2021-10-31 22:08:48
ACTIV_ERR4969040
* 2021-10-31 22:08:48
ACTIV_ERR4969039
* 2021-10-31 22:08:48
ACTIV_ERR4969190
* 2021-10-31 22:08:48
ACTIV_ERR4969189
* 2021-10-31 22:08:48
ACTIV_ERR4969187
* 2021-10-31 22:08:48
ACTIV_ERR4969185
* 2021-10-31 22:08:48
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* 2021-10-31 22:08:48
ACTIV_ERR4969177
* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
ACTIV_ERR4969072
* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
ACTIV_ERR4969043
* 2021-10-31 22:08:47
ACTIV_ERR4969005
* 2021-10-31 22:08:47
ACTIV_ERR4969183
* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
ACTIV_ERR5505512
* 2021-10-31 22:08:47
ACTIV_ERR5501241
* 2021-10-31 22:08:47
ACTIV_ERR4807226
* 2021-10-31 22:08:47
ACTIV_ERR4365335
* 2021-10-31 22:08:47
ACTIV_ERR5514445
* 2021-10-31 22:08:47
ACTIV_ERR4440121
* 2021-10-31 22:08:47
ACTIV_ERR4440037
* 2021-10-31 22:08:47
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* 2021-10-31 22:08:47
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
ACTIV_ERR5495833
* 2021-10-31 22:08:46
ACTIV_ERR4780288
* 2021-10-31 22:08:46
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* 2021-10-31 22:08:46
ACTIV_ERR4439934
* 2021-10-31 22:08:46
ACTIV_ERR4439752
* 2021-10-31 22:08:45
ACTIV_ERR4969047
* 2021-10-31 22:08:45
ACTIV_ERR5495454
* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
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* 2021-10-31 22:08:39
ACTIV_ERR4365125
* 2021-10-31 22:08:38
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* 2021-10-31 22:08:38
ACTIV_ERR5505783
* 2021-10-31 22:08:38
ACTIV_ERR4364963
* 2021-10-31 21:57:29
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* 2021-10-31 21:57:29
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* 2021-10-31 21:57:29
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* 2021-10-31 21:57:29
ACTIV_ERR4969141
* 2021-10-31 21:57:28
ACTIV_SRR13870638
* 2021-10-31 21:57:28
ACTIV_SRR13870636
* 2021-10-31 21:57:28
ACTIV_SRR13870635
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
ACTIV_SRR13870626
* 2021-10-31 21:57:28
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* 2021-10-31 21:57:28
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* 2021-10-31 21:57:28
ACTIV_ERR4969132
* 2021-10-31 21:57:27
ACTIV_SRR13870634
* 2021-10-31 21:57:27
ACTIV_SRR13870633
* 2021-10-31 21:57:27
ACTIV_SRR13870626
* 2021-10-31 21:57:27
ACTIV_SRR13870626
* 2021-10-31 21:57:27
ACTIV_SRR13870626
* 2021-10-21 15:57:54
CDC_test_dataset4_SRR14241199
* 2021-10-21 15:57:41
CDC_test_dataset4_SRR13606410
* 2021-10-21 15:57:22
CDC_test_dataset4_SRR13603869
* 2021-10-21 15:57:15
CDC_test_dataset4_SRR13511054
* 2021-10-21 15:57:13
CDC_test_dataset4_SRR13500958
* 2021-10-21 15:57:10
CDC_test_dataset4_SRR13422802
* 2021-10-21 15:56:55
CDC_test_dataset4_SRR13422799
* 2021-10-21 15:56:23
CDC_test_dataset4_ERR5771988
* 2021-10-21 15:56:18
CDC_test_dataset4_ERR5749609
* 2021-10-21 15:56:06
CDC_test_dataset4_ERR5743893
* 2021-10-21 15:55:42
CDC_test_dataset4_ERR5743043
* 2021-10-21 15:55:09
CDC_test_dataset4_ERR5691945
* 2021-10-21 15:54:55
CDC_test_dataset4_ERR5556343
* 2021-10-21 15:54:40
CDC_test_dataset4_ERR5405022
* 2021-10-21 15:54:17
CDC_test_dataset4_ERR5181360
* 2021-10-21 15:54:11
CDC_test_dataset4_ERR5181310
* 2021-10-21 15:40:08
CDC_test_dataset5_SRR13690340
* 2021-10-21 15:40:07
CDC_test_dataset5_SRR13690003
* 2021-10-21 15:40:01
CDC_test_dataset5_SRR13689874
* 2021-10-21 15:39:41
CDC_test_dataset5_SRR13687078
* 2021-10-21 15:39:16
CDC_test_dataset5_SRR13668148
* 2021-10-21 15:38:44
CDC_test_dataset5_SRR13574337
* 2021-10-21 15:38:38
CDC_test_dataset5_SRR13527262
* 2021-10-21 15:38:37
CDC_test_dataset5_SRR13526755
* 2021-10-21 15:38:25
CDC_test_dataset5_SRR13486908
* 2021-10-21 15:38:14
CDC_test_dataset5_SRR13433883
* 2021-10-21 15:38:01
CDC_test_dataset5_SRR13373851
* 2021-10-21 15:37:49
CDC_test_dataset5_SRR13358209
* 2021-10-21 15:37:40
CDC_test_dataset5_SRR13297857
* 2021-10-21 15:37:34
CDC_test_dataset5_SRR13297853
* 2021-10-21 15:37:18
CDC_test_dataset5_SRR13195337
* 2021-10-21 15:37:05
CDC_test_dataset5_SRR13195265
* 2021-10-21 15:37:00
CDC_test_dataset5_SRR13195052
* 2021-10-21 15:36:51
CDC_test_dataset5_SRR13193342
* 2021-10-21 15:36:24
CDC_test_dataset5_SRR13129709
* 2021-10-21 15:36:09
CDC_test_dataset5_SRR13126740
* 2021-10-21 15:35:47
CDC_test_dataset5_SRR13089080
* 2021-10-21 15:35:22
CDC_test_dataset5_SRR13062553
* 2021-10-21 15:35:17
CDC_test_dataset5_SRR13004400
* 2021-10-21 15:35:06
CDC_test_dataset5_SRR13001544
* 2021-10-21 15:34:48
CDC_test_dataset5_SRR12901576
* 2021-10-21 15:34:45
CDC_test_dataset5_SRR12833927
* 2021-10-21 15:34:34
CDC_test_dataset5_SRR12833718
* 2021-10-21 15:34:33
CDC_test_dataset5_SRR12774785
* 2021-10-21 15:34:30
CDC_test_dataset5_SRR12763543
* 2021-10-21 15:34:26
CDC_test_dataset5_SRR12751757
* 2021-10-21 15:34:26
CDC_test_dataset5_SRR12733606
* 2021-10-21 15:33:34
CDC_test_dataset5_SRR12661075
* 2021-10-21 15:33:29
CDC_test_dataset5_SRR12530461
* 2021-10-21 15:33:29
CDC_test_dataset5_SRR12212912
* 2021-10-21 15:33:19
CDC_test_dataset5_SRR12192434
* 2021-10-21 15:33:07
CDC_test_dataset5_SRR12162365
* 2021-10-21 15:32:58
CDC_test_dataset5_SRR11915959
* 2021-10-21 15:32:57
CDC_test_dataset5_SRR11577968
* 2021-10-21 15:32:57
CDC_test_dataset5_SRR11494584
* 2021-07-30 21:43:44
SRR15085319
* 2021-07-30 21:39:42
SRR15121725
* 2021-07-30 21:39:41
SRR15023323
* 2021-07-30 21:38:42
SRR15085317
* 2021-07-30 21:36:43
SRR15085360
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SRR15023416
* 2021-07-30 21:34:43
SRR15121740
* 2021-07-30 21:34:42
SRR15085363
* 2021-07-30 21:31:41
SRR15121737
* 2021-07-30 21:30:10
SRR15085591
* 2021-07-30 21:30:02
SRR15155108
* 2021-07-30 21:29:45
SRR15085583
* 2021-07-30 21:29:36
SRR15086265
* 2021-07-30 21:15:22
SRR15022313
* 2021-07-30 21:15:22
SRR15022876
* 2021-07-30 21:15:22
SRR15121763
* 2021-07-14 20:23:23
Researchspecificpopulation7
* 2021-07-14 07:54:39
Researchspecificpopulation6
* 2021-07-14 07:53:26
Researchspecificpopulation5
* 2021-07-14 07:51:58
Researchspecificpopulation3
* 2021-07-14 07:43:36
Samplespecificpopulation
* 2021-05-10 18:15:12
NM2021052580
* 2021-05-10 18:14:57
NM2021053044
* 2021-05-10 18:14:42
NM2021053982
* 2021-05-10 18:14:42
NM2021053203
* 2021-05-10 18:14:12
NM2021061184
* 2021-05-10 18:13:43
NM2021061511
* 2021-05-10 18:11:42
NM2021059733
* 2021-05-10 18:10:42
NM2021052971
* 2021-05-10 18:09:57
NM2021061122
* 2021-05-10 18:09:57
NM2021058899
* 2021-05-10 18:09:42
NM2021061324
* 2021-05-10 18:09:27
NM2021066375
* 2021-05-10 18:09:12
NM2021055380
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NM2021052578
* 2021-05-10 18:07:57
NM2021061362
* 2021-05-10 18:06:42
NM2021052266
* 2021-05-10 18:05:57
NM2021052326
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NM2021052313
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NM2021060107
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NM2021061361
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NM2021052074
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NM2021054389
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NM2021052315
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NM2021054074
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NM2021054107
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NM2021054145
* 2021-05-10 17:59:12
NM2021059628
* 2021-05-10 17:58:42
NM2021060531
* 2021-05-10 17:57:57
NM2021063879
* 2021-05-10 17:57:57
NM2021063877
* 2021-05-10 17:56:42
NM2021052026
* 2021-05-10 17:56:27
NM2021055666
* 2021-05-10 17:56:27
NM2021053119
* 2021-05-10 17:53:58
NM2021059651
* 2021-05-10 17:53:58
NM2021059284
* 2021-05-10 17:53:58
NM2021058801
* 2021-04-20 20:48:19
ERR4807186_kmer_positive_reads
* 2020-10-16 18:15:30
VIC07_Articv1_ONT
* 2020-10-14 11:10:59
NM2020016449
* 2020-10-14 11:10:29
NM2020016419
* 2020-10-14 11:10:14
NM2020016415
* 2020-10-14 11:09:59
NM2020016089
* 2020-10-14 11:09:44
NM2020016077
* 2020-10-14 11:09:14
NM2020016075
* 2020-10-14 11:08:30
NM2020016074
* 2020-10-14 10:56:45
NM2020016073
* 2020-07-02 22:07:09
EPI_ISL_485872
Job Progress
* ACTIV_ERR4365209
* Download SRA
* Count Fastq
* Quality Trim and Filter
* Reads Mapping To Reference
* Variant Analysis
* Generate JBrowse Tracks
* HTML Report
* Last checked: 2021-12-30 12:04:05
* EDGE Server Usage
* CPU
30.5 %
* MEM
8.7 %
* DISK
65.0 %
* Action
* View live log
* Force this project to rerun
* Reconfig project (BETA)
* Interrupt running project
* Delete entire project
* Empty project outputs
* Move to the archive storage
* Share project
* Unshare project
* Make project public
* Rename Project
* Rerun Pangolin
* Metadata Aciton
* Update Metadata
* Upload to GISAID and NCBI
* Upload to NCBI SRA
2.0.0
New to EDGE?
2.4.0
Run EDGE
EDGE bioinformatics
1.0.0
Upload Data
Allowed File types are fastq, fasta, genbank, gff, xlsx and text
(txt,config,ini) and can be in gzip format.
Nano-EDGE
Run EDGE for Nanopore dataset.
1.0.0
Project List
sra-EDGE
Run EDGE for Sequence Read Archive
1.0.0
Reports
Create summary tables for multiple projects.
EMPOWERING THE DEVELOPMENT OF GENOMICS EXPERTISE
EDGE COVID-19 is a tailored bioinformatics platform based on the more flexible
and fully open-source EDGE Bioinformatics software (Li et al. 2017). This
mini-version consists of a user-friendly GUI that drives standardized workflows
for genome reference-based 'assembly' and preliminary analysis of Illumina or
Nanopore data for SARS-CoV-2 genome sequencing projects. The result is a final
SARS-CoV-2 genome ready for submission to GISAID and/or GenBank.
The default workflow in EDGE COVID-19 includes:
1. data quality control (QC) and filtering,
2. alignment of reads to the original (first available) reference genome
(NC_045512.2, we removed the PolyA tail from the 3' end (33 nt)),
3. creation of a consensus genome sequence based on the read alignments, and
4. a Single Nucleotide Polymorphism and Variant analyses, with some detail such
as location and resulting coding differences if any.
The EDGE COVID-19 platform can accommodate Illumina or ONT data, including ONT
data from the SARS-CoV-2 ARTIC network sequencing protocols. Users can
input/upload Illumina or Nanopore sequencing FASTQ files (and/or download from
NCBI SRA). For Illumina data, default analyses include only read QC, read
mapping to the reference, and SNP/variant analysis. For ONT data, the data must
be demultiplexed prior to uploading; the samples will be processed individually.
The SNP/variant calling is not on by default for ONT. However, other functions
(e.g. de novo assembly for whole genome data) are also available for both
sequencing platforms. While command line execution is possible (see here and
here), the GUI provides an easy data submission and results viewing platform,
with the graphical and tabular views of variant/SNP data and a genome browser to
view read coverage and location of SNPs or variants, as well as the reference
annotations.
This light-weight version is a Docker container, able to run on any local
hardware infrastructure or in the cloud. We have tested this Docker container on
laptops and cloud, using several Illumina (e.g. SRR11177792) and ONT (e.g.
SRR11300652) datasets.
Note: For EDGE Bioinformatics users who would also like to use the phylogeny or
read- and assembly-based taxonomy classification tools to identify all organisms
that may be present within complex samples, we recommend using the original EDGE
Bioinformatics platform which harbors several tools and associated (large)
databases that enable such a search. In initial tests of taxonomy classification
of SARS-CoV-2 samples (with no SARS-CoV-2 genomes in any of the databases), we
recover SARS coronavirus and Bat Coronavirus as the nearest neighbor.
FEATURES OF EDGE
* No need for high-level bioinformaticists
* Allow users to address a wide range of use cases including the
assembly/annotation and comparison of novel genomes, and the characterization
of complex clinical or environmental samples
* Focus on accurate and rapid analysis
* Enables sequencing as a solution in facilities where human-resources, space,
bandwidth, and time are limited
IMPLEMENTATION
* EDGE Bioinformatics is built around a collection of publicly available,
open-source software packaged or in-house developed tools/algorithms/scripts
to process FASTQ data
* The EDGE bioinformatics web-based graphic user interface is primarily
implemented using the JQuery Mobile javascript framework and HTML5 on the
client-side, and implements perl CGI using Apache or Python on the
server-side
* Due to the involvement of several memory/time consuming steps, we normally
recommend computers with at least 8GB memory and 8 CPUs, though we typically
use on servers with a minimum of 256GB memory with 64 CPUs
DOWNLOAD & UPDATES
EDGE COVID-19 Docker image: location and instructions.
The Source code: LANL-Bioinformatics GitHub site.
TUTORIAL & HELP
* The detailed user guide can be found in here
* The EDGE tutorial video series for the original EDGE platform hosted in
Youtube.
* User discussion group can be found here or you can contact us at
edge-covid19@lanl.gov.
PUBLICATION
Lo, Chien-Chi, Migun Shakya, Karen Davenport, Mark C. Flynn, Jason D. Gans, Adán
Myers yGutiérrez, Bin Hu, Po-E Li, Elais Player Jackson, Yan Xu and Patrick S.
G. Chain. EDGE COVID-19: A Web Platform to generate submission-ready genomes for
SARS-CoV-2 sequencing efforts. (2020). https://arxiv.org/abs/2006.08058
This research was supported by LANL (20200732ER), by DTRA (CB10152 and CB10623)
and by the DOE Office of Science (KP160101), through the National Virtual
Biotechnology Laboratory, a consortium of DOE national laboratories focused on
response to COVID-19, with funding provided by the Coronavirus CARES Act.
INPUT YOUR SAMPLE
EDGE requires sequence data files in FASTQ format. EDGE accepts both paired-end
and single-end sequence data files. User Guide
The Qiime2 pipeline requires sequence data files in FASTQ format and a mapping
file. The sequence file is either paired-end or single-end sequences.Or
directory with demultiplexed fastq files. Please see the documentation for more
information.
The DETEQT is a pipeline for diagnostic targeted sequencing adjudication. Please
see the documentation for more information.
The PiReT is a pipeline for Reference based Transcriptomics analysis. Please see
the documentation for more information.
INPUT RAW READS CLICK TO COLLAPSE CONTENTS
Project/Run Name
Description
Amplicon Type
16s (GreenGenes)
16s/18s (SILVA)
16s V3-V4 (SILVA)
Fungal ITS
Input Source
READS / FASTQ
NCBI SRA
Platform
Nanopore
Illumina
PacBio
SRA Accession
(Internet required) Input SRA accessions (comma separate for > 1 input) support
studies (SRP*/ERP*/DRP*), experiments (SRX*/ERX*/DRX*), samples
(SRS*/ERS*/DRS*), runs (SRR*/ERR*/DRR*), or submissions (SRA*/ERA*/DRA*). ex:
SRR11241255
Contig Fasta File
file
Reads Type
De-multiplexed Reads Dir
Paired Reads
Unpaired Reads
Sequencing Reads:
Pair-1 FASTQ File
file
Pair-2 FASTQ File
file Delete
and/or
Single-end FASTQ File
file Delete
Directory
Dir
Metadata Mapping File
file Delete
Targeted Amplicon References
file
| additional options |
Add Paired-end Input Add Single-end Input Add Mapping File Field
Use # of CPUs
Config File
file
Your customized parameters can be used again. You can utilize the file selector
above to upload a standard config file generated by EDGE bioinformatics.
BATCH PROJECT SUBMISSION CLICK TO EXPAND CONTENTS
Run EDGE with Multiple projects using a tools set configuration. Click Download
[Sample File] to see the example.
Batch Excel File
file
INPUT METADATA CLICK TO EXPAND CONTENTS
Virus detail
Virus name
Passage details/history
Sample information
Collection date
Location
Host
Gender
Select Gender Select Gender Male Female Other Unknown
Patient age
Patient status
Select Status Select Status Hospitalized Released Live Deceased Unknown
Sequencing Technology
CHOOSE PROCESSES / ANALYSES
EDGE provides many modules to do various analyses. You can choose to run or skip
a specific process. Parameters/options are provided for most of the analyses.
You can click here to turn all on, expand all sections or close all sections.
OFFON
ONOFF
PRE-PROCESSING
CLICK TO EXPAND CONTENTS
Quality Trim and Filter
Stitch Paired-End Reads
Host Removal
Run Quality Trim and Filter
Yes
No
Quality Offset
AutoCheck
Phred+33
Phred+64
Trim Quality Level
Clear text
Average Quality Cutoff
Clear text
Minimum Read Length
Clear text
"N" Base Cutoff
Clear text
Low Complexity Filter
Trim Sequencing Primers
V1
V2
V3
V4
CDC
SWIFT
Freed
Varskip_V1a
Off
Primer Trim Method
Align Trim
FaQCs
Primer BED
file
Primer FASTA
file
Trim polyA
On
Off
Cut #bp from 5'-end
Clear text
Cut #bp from 3'-end
Clear text
Run Stitch PE Reads
Yes
No
N-percent Max Difference
Clear text
N-minimum Overlap
Clear text
Use joined PE reads only
Yes
No
Human Host Removal
Yes
No
Additional Host FASTA File
file
Similarity (%)
Clear text
OFFON
ONOFF
ASSEMBLY AND ANNOTATION
CLICK TO EXPAND CONTENTS
Assembly
Annotation
Binning
Bypass Assembly And Use Pre-assembled Contigs
Yes
No
Contig Fasta File
file
Assembler
IDBA_UD
SPAdes
MEGAHIT
UniCycler
LRASM
Unicycler is an assembly pipeline for bacterial genomes. It can assemble
Illumina-only read sets where it functions as a SPAdes-optimise. For the best
possible assemblies, give it both Illumina reads and long reads, and it will
conduct a hybrid assembly.
Bridging mode
Normal
Conservative
Bold
Long Reads Fasta/q
file
Minimum Long Reads Cutoff (bp)
Clear text
LRASM is designed for long noise reads such as reads from Nanopore and it
assemble fastq/fasta formatted reads using miniasm/wtdbg2/flye and use racon to
perform consensus.
Algorithm
miniasm
wtdbg2
flye
metaFlye
Error Correction
Yes
No
Preset
Nanopore
Pacbio
Num of Iteration of Consensus
Clear text
IDBA_UD performs well on isolates as well as metagenomes but it may not work
well on very large genomes.
Minimum Kmer Length
Clear text
Maximum Kmer Length
Clear text
Step Size
Clear text
SPAdes performs well on isolates as well as single cell data but it may not work
on larger genomes, and it takes more computational resource. PacBio CLR and
Oxford Nanopore reads are used for gap closure and repeat resolution.
Algorithm
Default Default Single-cell (MDA) Metagenome (metaSPAdes) Plasmids
(plasmidSPAdes) RNA (rnaSPAdes)
Pacbio Subreads Fasta/q
file
Nanopore Reads Fasta/q
file
MEGAHIT is an ultra-fast single-node solution for large and complex metagenomics
assembly via succinct de Bruijn graph which achieves low memory assembly.
Preset
meta meta meta-sensitive meta-large
Minimum Contig Length
Clear text
Validation Aligner
Bowtie 2
BWA mem
Minimap2
| additional options |
Aligner Options
Extract Unmapped/Unassembled Reads
Yes
No
Annotation
Yes
No
EDGE will use RATT to transfer the annotation from the reference genome,
NC_045512.2.
Minimum Contig Length for Annotation
Clear text
Annotation Tool
Prokka
RATT
Specify Kingdom
Archaea
Bacteria
Mitochondria
Viruses
Metagenome
KEGG Pathway View
Yes
No
Annotation Source Genbank
file
Secondary Metabolite Analysis Parameters
Taxon
Bacteria
Fungi
Known ClusterBlast
On
Off
Sub ClusterBlast
On
Off
smCoG analysis
On
Off
Active Site Finder
On
Off
ClusterBlast
On
Off
Whole-genome PFAM analysis
On
Off
Detect TTA codons
On
Off
Cluster-border prediction based on transcription factor binding sites (CASSIS)
On
Off
| additional options |
Trusted HMM for Prokka
file
Binning
Yes
No
Minimum Contig Length
Clear text
Maximum EM Algorithm Iteration
Clear text
EM Probability
Marker Gene Sets
107
40
Abundance File
file
CheckM
Yes
No
OFFON
ONOFF
REFERENCE-BASED SARS-COV-2 GENOME ANALYSIS
CLICK TO COLLAPSE CONTENTS
Preselected NCBI RefSeq Reference Genome
Yes
No
Select Additional GenBank Reference Genome(s) (Optional)
Select additional reference genome(s)...0 Select additional reference
genome(s)...
Extra Reference Genome (Optional)
file Add
Read Aligner
Bowtie 2
BWA mem
Minimap2
Variant Call
Yes
No
Consensus Fasta
Yes
No
Minimum Coverage
Clear text
Alternate Base Threshold
Indels Threshold
Lineage Assignment Mode
Usher
PangoLearn
| additional options |
Consensus Generation Options
Minimum mapQ
Clear text
Maximum Coverage
Clear text
Minimum baseQ
Clear text
Disable BAQ
Yes
No
Remove PCR Duplicates
Yes
No
Homopolymer Filter
Yes
No
StrandBias Filter
Yes
No
Aligner Options
MaxClip
Clear text
Extract Mapped Reads
Yes
No
Extract Unmapped Reads
Yes
No
Variant QUAL
Clear text
Ploidy
Haploid
Diploid
OFFON
ONOFF
TAXONOMY CLASSIFICATION
CLICK TO EXPAND CONTENTS
a. Read-based Taxonomy Classification
EDGE will use all reads by default. You can change the behavior to use reads
that are unmapped to the reference if Reference-based Analysis is on.
Always Use All Reads
Yes
No
Classification Tools
Run With Following Databases
GOTTCHA Genus, GOTTCHA Species , GOTTCHA Strain, GOTTCHA Genus, GOTTCHA
Species, GOTTCHA Strain, Reads Mapping (BWA against RefSeq), MetaPhlAn2,
Kraken29 Choose Classification Tools: GOTTCHA Genus GOTTCHA Species GOTTCHA
Strain GOTTCHA Genus GOTTCHA Species GOTTCHA Strain GOTTCHA2 Species Reads
Mapping (BWA against RefSeq) MetaPhlAn2 Kraken2 DIAMOND (Amino acid-based
classification)
| additional options |
Splitrim Quality Level
Clear text
Custom DB Tool
Reads Mapping (BWA against custom DB) GOTTCHA Bacteria Genus GOTTCHA
Bacteria Species GOTTCHA Bacteria Strain GOTTCHA Virus Genus GOTTCHA Virus
Species GOTTCHA Virus Strain Reads Mapping (BWA against custom DB)
MetaPhlAn2 Kraken Add
Custom Database
file
b. Contig-based Taxonomy Classification
Contigs Classification
Yes
No
OFFON
ONOFF
PHYLOGENETIC ANALYSIS
CLICK TO EXPAND CONTENTS
EDGE supports 5 pre-computed databases for SNP phylogeny analysis and two tree
builders. FastTree is faster and RAxML is slower but more accurate.
Tree Build Method
FastTree
RAxML
Pre-built SNP DB
Select a Pathogen... Select a Pathogen... Ecoli Yersinia Francisella Brucella
Bacillus
or
Select/Add Genomes or SRA Reads: The same species or at least within the same
genus are recommended.
Select Genome(s)
Search genomes...0 Search genomes...
Select A Reference Genome from Selected Genomes
Random Random
Add Genome(s)
file Add
SRA Accessions
Bootstrap
Yes
No
Bootstrap Number
Clear text
OFFON
ONOFF
GENE FAMILY ANALYSIS
CLICK TO EXPAND CONTENTS
a. Read-based Gene Family Analysis
EDGE will use ShortBRED to search the reads for Antibiotic Resistance genes
from ARDB and Resfams and for Virulence genes from VFDB.
Reads Gene Family Analysis
Yes
No
b. Contig-based (CDS) Gene Family Analysis
EDGE will use ShortBRED to search the CDSs on the contigs for Virulence
genes from VFDB.
EDGE will use RGI (Resistance Gene Identifier) to search the CDSs on the
contigs for Antibiotic Resistance genes from CARD.
CDS Gene Family Analysis
Yes
No
| additional options |
ShortBRED Minimum Percent Identity
ShortBRED Minimum Percent Length
OFFON
ONOFF
PCR PRIMER ANALYSIS
CLICK TO EXPAND CONTENTS
a. Primer Validation
b. Primer Design
Run Primer Validation
Yes
No
Given a primer file, EDGE will run validation of the primer pair to the
reference and/or assembled contigs, as available.
Primer Fasta Sequences
file
Maximum Mismatch
0
1
2
3
4
Run Primer Design
Yes
No
EDGE will design primers based on the assembled contigs.
Tm Optimum (C)
Clear text
Tm Range (C)
Length Optimum (bp)
Clear text
Length Range (bp)
Background Tm Differential (C)
Clear text
Number of Primer Pairs
Clear text
PARAMETERS CLICK TO COLLAPSE CONTENTS
a. Barcode Options
Barcode Fastq File
file
b. Reads Quality Control and Feature Table Construction
Quality Offset
Phred+33
Phred+64
Quality Control Method
DADA2
Deblur
Trim 5'end Forward
Clear text
Trim 5'end Reverse
Clear text
Truncation Len Forward
Clear text
Truncation Len Reverse
Clear text
SE Trim Length
Clear text
PHRED Quality
Clear text
Max "N" base
Clear text
Min Per Read Length Fraction
SE Truncation Len
Clear text
c. Sampling
Sampling Depth
Clear text
Auto-Adjust Sampling Depth
Yes
No
PARAMETERS CLICK TO COLLAPSE CONTENTS
Platform
Illumina
Nanopore
Mode
Paired-End
Single-End
Quality Calculation Cutoff
Depth Filter
Clear text
| additional options |
Read Length Filter
Clear text
The following parameters will affect how the Quality Calcuation derived. The
four weight parameters should sum up to 1. Mouse over the label to see the
notes.
Expected Coverage
Expected Identity
Expected BaseQ
Expected Mapping Quality
Coverage Weight
Identity Weight
BaseQ Weight
MapQ Weight
PARAMETERS CLICK TO COLLAPSE CONTENTS
a. Required arguments
Kingdom
Prokarya
Eukarya
Both
Prokaryotic Reference Fasta
file
Prokaryotic Reference GFF
file
Eukaryotic Reference Fasta
file
Eukaryotic Reference GFF
file
b. Optional arguments
Strandedness
Not Stranded
Forward
Reverse
Method
edgeR edgeR DESeq2 ballgown DEedge balledgeR DEgown
HISAT2 index file
file
Q-value
Submit
Reset
Save modified parameters
UPLOAD FILES
Max file size is 1gb and total user space up to 1gb. Allowed File types are
fastq, fasta, genbank, gff, xlsx and text (txt,bed,config,ini) and can be in
gzip format. Files will be kept for 180 days.
You are not logged in or your browser doesn't have Flash, Silverlight or HTML5
support.
ALTERNATIVE UPLOADING METHODS
Web uploader is designed to upload small files. When the sizes of uploading
files are >1000MB, please use one of following options:
* Directly copy files to user's MyUploads directory from the host OS (mounted
EDGE_input directory while docker run):
- The path is:
/path/to/EDGE_input//MyUploads/
- For example:
cp /path/to/your_seq.fastq /path/to/EDGE_input//MyUploads/
EDGESITE
Please fill out this form before using 'Run EDGE'.
Organization Full Name
Acronym
Location
Enable Sample Metadata?
Yes
No
Share Sample Metadata/Pathogens with BSVE?
Yes
No
Auto Submit Sample Metadata/Pathogens?
Yes
No
Sumbit
Reset
Questions? Please contact us at edge-covid19@lanl.gov.
EDGE-UI v2.4.0 build 20211217
No text
SELECT GENDER
* Select Gender
* Male
* Female
* Other
* Unknown
SELECT STATUS
* Select Status
* Hospitalized
* Released
* Live
* Deceased
* Unknown
* Default
* Single-cell (MDA)
* Metagenome (metaSPAdes)
* Plasmids (plasmidSPAdes)
* RNA (rnaSPAdes)
* meta
* meta-sensitive
* meta-large
SELECT ADDITIONAL REFERENCE GENOME(S)...
Close
Clear text
Select All | None
* Select additional reference genome(s)...
CHOOSE CLASSIFICATION TOOLS:
Close
* Choose Classification Tools:
* GOTTCHA Bacterial Databases
* GOTTCHA Genus
* GOTTCHA Species
* GOTTCHA Strain
* GOTTCHA Viral Databases
* GOTTCHA Genus
* GOTTCHA Species
* GOTTCHA Strain
* GOTTCHA2 BacteriaViruses Databases
* GOTTCHA2 Species
* Reads Mapping
* Reads Mapping (BWA against RefSeq)
* Other Tools
* MetaPhlAn2
* Kraken2
* DIAMOND (Amino acid-based classification)
* GOTTCHA Bacteria Genus
* GOTTCHA Bacteria Species
* GOTTCHA Bacteria Strain
* GOTTCHA Virus Genus
* GOTTCHA Virus Species
* GOTTCHA Virus Strain
* Reads Mapping (BWA against custom DB)
* MetaPhlAn2
* Kraken
SEARCH GENOMES...
Close
Clear text
Select All | None
* Search genomes...
* edgeR
* DESeq2
* ballgown
* DEedge
* balledgeR
* DEgown
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* data
* projects
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