DFAST_VRL Viral Genome Annotation

<!DOCTYPE html> <html> <head>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-109268803-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-109268803-1'); </script> <title>DFAST_VRL Viral Genome Annotation</title> <meta name="viewport" content="width=device-width, initial-scale=1.0">  <link href="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet"> <link rel="shortcut icon" href="/static/favicon.ico" type="image/x-icon"> <link rel="icon" href="/static/favicon.ico" type="image/x-icon"> <style type="text/css"> .container {width: 95%;} </style> </head> <body> <nav class="navbar navbar-inverse navbar-static-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a style="margin-left: -20px; margin-top: -8px" class="navbar-brand" href="/"><img height="30px" src="/static/DFAST_inverse.png" class="" alt="dfast_logo"></a> </div> <div class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false" id="analysis-dropdown">Analysis <span class="caret"></span></a> <ul class="dropdown-menu" role="menu"> <li><a href="/dfc/">Genome Annotation</a></li> <li class="divider"></li> <li><a href="/dfv/submit/">Genome Annotation for SARS-CoV-2</a></li> <li><a href="/dfv/vadr/">NCBI VADR (Beta, for viral sequences)</a></li> <li class="divider"></li> <li><a href="/dqc/submit/">Taxonomy/Completeness Check</a></li> </ul> </li> </ul> <ul class="nav navbar-nav navbar-right">  <li><a href="/dfc/distribution/">DFAST-core</a></li> <li><a href="/api/">API</a></li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false" id="help-dropdown">Help <span class="caret"></span></a> <ul class="dropdown-menu" role="menu"> <li><a href="/about">About DFAST</a></li> <li><a href="/faq">FAQ</a></li> <li><a href="/help_annotation">Help - DFAST</a></li> <li><a href="/help_login">Help - Login and Data Submission</a></li> </ul> </li> <li><a href="/auth/">Sign in</a></li> </ul> </div> </div> </nav> <div id="wrapper"> <div class="container"> <div class="page-container" id="page-container" style="width: 95%"> <div class="page-header"> <h2>DFAST_VRL</h2> <h5>SARS-CoV-2 genome annotation and data submission tool to DDBJ</h5> <p> DFAST_VRL consists of <a href="https://github.com/ncbi/vadr" target="blank_">NCBI VADR</a> and associated scripts to facilitate data submission to DDBJ.<br> Source code is available at Github: <a href="https://github.com/nigyta/dfast_vrl" target="blank_">nigyta/dfast_vrl</a><br> <br> If you want to try the pipeline, use sample files available from here: <a href="https://raw.githubusercontent.com/nigyta/dfast_vrl/main/examples/SRR10903401.meta_vrl.contig.fa" download="sars_cov2_contig.fa" target="blank_">Assembled contig file (FASTA)</a>, <a href="https://raw.githubusercontent.com/nigyta/dfast_vrl/main/examples/metadata.txt" download="metadata.txt" target="blank_">Metadata txt file</a> </p> </div> <form id="form_submit" action="" method="post" enctype="multipart/form-data"> <div class="row"> <div class="form-group col-xs-4"> <label for="queryFile" class="control-label"><label for="queryFile">Query File (Fasta format, required)</label></label> <input class="form-control" id="queryFile" name="queryFile" placeholder="" required style="height:40px" type="file"> </div> <div class="form-group col-xs-4"> <label for="metadataFile" class="control-label"><label for="metadataFile">Metadata File (Optional)</label></label> <input class="form-control" id="metadataFile" name="metadataFile" placeholder="" style="height:40px" type="file"> </div> </div> <div class="row"> <div class="col-xs-12">Only 1 genome per FASTA file is acceptable. (Complete genome in a single-FASTA file or draft genome in a multi-FASTA file)</div> </div> <br> <div class="row"> <div class="form-group col-xs-8"> <label for="isolate" class="control-label"><label for="isolate">Isolate</label></label> <input class="form-control" id="isolate" name="isolate" placeholder="e.g. SARS-CoV-2/human/Japan/SZ-NIG-12345/2022, NIG_12345" type="text" value=""> <p class="help-block">Optional, but it is recommended to specify a unique value to distinguish the sample. For DDBJ submission, specify an isolate name like 'SARS-CoV-2/host/location/isolate/date'.</p> </div> </div> <div class="row"> <div class="form-group col-xs-9"> <label for="title" class="control-label"><label for="title">Name/Title for the Job</label></label> <input class="form-control" id="title" name="title" placeholder="(optional)" type="text" value=""> </div> </div> <div class="row"> <div class="form-group col-xs-9"> <label for="mail" class="control-label"><label for="mail">Email Address</label></label> <input class="form-control" id="mail" name="mail" placeholder="E-mail notification will be sent to this address when the job is completed. (optional)" type="email" value=""> </div> </div> <div class="row"> <div class="form-group col-xs-9"> <hr style="margin-bottom: 0px" /> </div> </div> <div class="row"> <div class="col-xs-6" style=" margin-top: 10px"> <label> <input type="checkbox" id="modify_query_fasta" name="modify_query_fasta" value="y" > Modify query FASTA </label> <p style="margin-left: 20px;">When enabled, query FASTA will be modified based on the mapping result to the reference. (Will extract mapped regions and discard unmapped. If the mapped regions are fragmented, they will be scaffolded (concatenated) using runs of Ns representing assembly gaps of estimated length.)</p> </div> </div> <div class="row"> <div class="col-xs-6" style="margin-top: 10px"> <label> <input type="checkbox" id="disable_scaffolding" name="disable_scaffolding" value="y" > Disable scaffolding </label> <p style="margin-left: 20px;">Disable scaffolding process. Ignored when 'Modify query FASTA' is not specified.</p> </div> </div> <div class="row"> <div class="form-group col-xs-9"> <hr style="margin-bottom: 0px" /> </div> </div> <div class="form-group"> <input _name="_submit" class="btn btn-default btn-sm" id="_submit" name="submit_" type="submit" value="Run"> </div> <input id="csrf_token" name="csrf_token" type="hidden" value="IjlkZjJiMjQ2ZjNhMGYzYTMyNWQ4YzExYWZhMWU3YWMzODEzYTBlODMi.Z0bqvw.2ypf4Di0VATbBoxZTeQ8mE2rIRM"> </form> </div>  </div> </div> <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script> <script src="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js"></script> <script type="text/javascript" src="/static/chosen.jquery.min.js"></script> </body> </html>

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DFAST_VRL Viral Genome Annotation