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<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="#orgf894fd0">1. Workflow runs</a></li>
<li><a href="#org51b7162">2. FASTA files</a></li>
<li><a href="#org572ed1f">3. Metadata</a></li>
<li><a href="#org6b6b3d3">4. Pangenome</a>
<ul>
<li><a href="#org9f4caf2">4.1. Pangenome GFA format</a></li>
<li><a href="#org110286f">4.2. Pangenome in ODGI format</a></li>
<li><a href="#orgc83e017">4.3. Pangenome RDF format</a></li>
<li><a href="#org8b1948b">4.4. Pangenome Browser format</a></li>
</ul>
</li>
<li><a href="#org3848ad3">5. Log of workflow output</a></li>
<li><a href="#org3ecd561">6. All files</a></li>
<li><a href="#orga83843e">7. Planned</a>
<ul>
<li><a href="#orgcdeb8a1">7.1. Raw sequence data</a></li>
<li><a href="#org25b78b5">7.2. Multiple Sequence Alignment (MSA)</a></li>
<li><a href="#org02f524d">7.3. Phylogenetic tree</a></li>
<li><a href="#org78366fa">7.4. Protein prediction</a></li>
</ul>
</li>
<li><a href="#org3344c28">8. Source code</a></li>
<li><a href="#orgdd54c12">9. Citing PubSeq</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgf894fd0" class="outline-2">
<h2 id="orgf894fd0"><span class="section-number-2">1</span> Workflow runs</h2>
<div class="outline-text-2" id="text-1">
<p>
The last runs can be viewed <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects">here</a>. If you click on a run you can see
the workflows that ran under <code>Processes</code>. Output (also intermediate)
is listed under <code>Data collections</code>. All current data is listed
<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. Note that it takes time for a run to complete and show.
</p>
</div>
</div>
<div id="outline-container-org51b7162" class="outline-2">
<h2 id="org51b7162"><span class="section-number-2">2</span> FASTA files</h2>
<div class="outline-text-2" id="text-2">
<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-org572ed1f" class="outline-2">
<h2 id="org572ed1f"><span class="section-number-2">3</span> Metadata</h2>
<div class="outline-text-2" id="text-3">
<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
the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">DOCS</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-org6b6b3d3" class="outline-2">
<h2 id="org6b6b3d3"><span class="section-number-2">4</span> Pangenome</h2>
<div class="outline-text-2" id="text-4">
<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-org9f4caf2" class="outline-3">
<h3 id="org9f4caf2"><span class="section-number-3">4.1</span> Pangenome GFA format</h3>
<div class="outline-text-3" id="text-4-1">
<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-org110286f" class="outline-3">
<h3 id="org110286f"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3>
<div class="outline-text-3" id="text-4-2">
<p>
<a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph
implementation.
</p>
</div>
</div>
<div id="outline-container-orgc83e017" class="outline-3">
<h3 id="orgc83e017"><span class="section-number-3">4.3</span> Pangenome RDF format</h3>
<div class="outline-text-3" id="text-4-3">
<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-org8b1948b" class="outline-3">
<h3 id="org8b1948b"><span class="section-number-3">4.4</span> Pangenome Browser format</h3>
<div class="outline-text-3" id="text-4-4">
<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-org3848ad3" class="outline-2">
<h2 id="org3848ad3"><span class="section-number-2">5</span> Log of workflow output</h2>
<div class="outline-text-2" id="text-5">
<p>
Including in below link is a log file of the last workflow runs.
</p>
</div>
</div>
<div id="outline-container-org3ecd561" class="outline-2">
<h2 id="org3ecd561"><span class="section-number-2">6</span> All files</h2>
<div class="outline-text-2" id="text-6">
<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 id="outline-container-orga83843e" class="outline-2">
<h2 id="orga83843e"><span class="section-number-2">7</span> Planned</h2>
<div class="outline-text-2" id="text-7">
<p>
We are planning the add the following output (see also
</p>
</div>
<div id="outline-container-orgcdeb8a1" class="outline-3">
<h3 id="orgcdeb8a1"><span class="section-number-3">7.1</span> Raw sequence data</h3>
<div class="outline-text-3" id="text-7-1">
<p>
See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>.
</p>
</div>
</div>
<div id="outline-container-org25b78b5" class="outline-3">
<h3 id="org25b78b5"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>.
</p>
</div>
</div>
<div id="outline-container-org02f524d" class="outline-3">
<h3 id="org02f524d"><span class="section-number-3">7.3</span> Phylogenetic tree</h3>
<div class="outline-text-3" id="text-7-3">
<p>
See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>.
</p>
</div>
</div>
<div id="outline-container-org78366fa" class="outline-3">
<h3 id="org78366fa"><span class="section-number-3">7.4</span> Protein prediction</h3>
<div class="outline-text-3" id="text-7-4">
<p>
We aim to make protein predictions available.
</p>
</div>
</div>
</div>
<div id="outline-container-org3344c28" class="outline-2">
<h2 id="org3344c28"><span class="section-number-2">8</span> Source code</h2>
<div class="outline-text-2" id="text-8">
<p>
All source code for this website and tooling is available
from
<a href="https://github.com/arvados/bh20-seq-resource">https://github.com/arvados/bh20-seq-resource</a>
</p>
</div>
</div>
<div id="outline-container-orgdd54c12" class="outline-2">
<h2 id="orgdd54c12"><span class="section-number-2">9</span> Citing PubSeq</h2>
<div class="outline-text-2" id="text-9">
<p>
See the <a href="./about">FAQ</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 2020-11-05 Thu 05:26</small>.
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