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+<head>
+<!-- 2020-05-24 Sun 11:11 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>Download</title>
+<meta name="generator" content="Org mode" />
+<meta name="author" content="Pjotr Prins" />
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+</style>
+<script type="text/javascript">
+/*
+@licstart The following is the entire license notice for the
+JavaScript code in this tag.
+
+Copyright (C) 2012-2020 Free Software Foundation, Inc.
+
+The JavaScript code in this tag is free software: you can
+redistribute it and/or modify it under the terms of the GNU
+General Public License (GNU GPL) as published by the Free Software
+Foundation, either version 3 of the License, or (at your option)
+any later version. The code is distributed WITHOUT ANY WARRANTY;
+without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
+
+As additional permission under GNU GPL version 3 section 7, you
+may distribute non-source (e.g., minimized or compacted) forms of
+that code without the copy of the GNU GPL normally required by
+section 4, provided you include this license notice and a URL
+through which recipients can access the Corresponding Source.
+
+
+@licend The above is the entire license notice
+for the JavaScript code in this tag.
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+/*]]>*///-->
+</script>
+</head>
+<body>
+<div id="content">
+<h1 class="title">Download</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#orge184013">1. FASTA files</a></li>
+<li><a href="#orgc0ce14b">2. Metadata</a></li>
+<li><a href="#org52c7997">3. Pangenome</a>
+<ul>
+<li><a href="#orgba61745">3.1. Pangenome GFA format</a></li>
+<li><a href="#org6474dfc">3.2. Pangenome in ODGI format</a></li>
+<li><a href="#orge3a3726">3.3. Pangenome RDF format</a></li>
+<li><a href="#org359cc22">3.4. Pangenome Browser format</a></li>
+</ul>
+</li>
+<li><a href="#org488e901">4. Log of workflow output</a></li>
+<li><a href="#orga53b821">5. All files</a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-orge184013" class="outline-2">
+<h2 id="orge184013"><span class="section-number-2">1</span> FASTA files</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+The <b>public sequence resource</b> provides all uploaded sequences as
+FASTA files. They can be referred to from metadata individually. We
+also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">FASTA download</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc0ce14b" class="outline-2">
+<h2 id="orgc0ce14b"><span class="section-number-2">2</span> Metadata</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which
+can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL
+endpoint ourselves which can be queried from
+<a href="http://sparql.genenetwork.org/sparql/">http://sparql.genenetwork.org/sparql/</a>. Query examples can be found in
+our <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">BLOG</a>.
+</p>
+
+<p>
+The Swiss Institute of Bioinformatics has included this data in
+<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part of <a href="https://www.uniprot.org/">Uniprot</a>.
+</p>
+
+<p>
+An RDF file that includes the sequences themselves in a variation
+graph can be downloaded from below Pangenome RDF format.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org52c7997" class="outline-2">
+<h2 id="org52c7997"><span class="section-number-2">3</span> Pangenome</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+Pangenome data is made available in multiple guises. Variation graphs
+(VG) provide a succinct encoding of the sequences of many genomes.
+</p>
+</div>
+
+<div id="outline-container-orgba61745" class="outline-3">
+<h3 id="orgba61745"><span class="section-number-3">3.1</span> Pangenome GFA format</h3>
+<div class="outline-text-3" id="text-3-1">
+<p>
+<a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed
+by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org6474dfc" class="outline-3">
+<h3 id="org6474dfc"><span class="section-number-3">3.2</span> Pangenome in ODGI format</h3>
+<div class="outline-text-3" id="text-3-2">
+<p>
+<a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimized dynamic genome/graph
+implementation.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orge3a3726" class="outline-3">
+<h3 id="orge3a3726"><span class="section-number-3">3.3</span> Pangenome RDF format</h3>
+<div class="outline-text-3" id="text-3-3">
+<p>
+An RDF file that includes the sequences themselves in a variation
+graph can be downloaded from
+<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">relabeledSeqs-dedup-relabeledSeqs-dedup.ttl.xz</a>.
+</p>
+</div>
+</div>
+
+
+<div id="outline-container-org359cc22" class="outline-3">
+<h3 id="org359cc22"><span class="section-number-3">3.4</span> Pangenome Browser format</h3>
+<div class="outline-text-3" id="text-3-4">
+<p>
+The many JSON files that are named as
+<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">results/1/chunk001200.bin1.schematic.json</a> are consumed by the
+Pangenome browser.
+</p>
+</div>
+</div>
+</div>
+
+<div id="outline-container-org488e901" class="outline-2">
+<h2 id="org488e901"><span class="section-number-2">4</span> Log of workflow output</h2>
+<div class="outline-text-2" id="text-4">
+<p>
+Including in below link is a log file of the last workflow runs.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orga53b821" class="outline-2">
+<h2 id="orga53b821"><span class="section-number-2">5</span> All files</h2>
+<div class="outline-text-2" id="text-5">
+<p>
+<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a>
+</p>
+</div>
+</div>
+</div>
+<div id="postamble" class="status">
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-24 Sun 11:11</small>.
+</div>
+</body>
+</html>
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-08 05:24:28 +0000