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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="#orgcde4e6b">1. Workflow runs</a></li>
<li><a href="#org1b46d7e">2. FASTA files</a></li>
<li><a href="#orgf2db570">3. Metadata</a></li>
<li><a href="#org9f89b24">4. Pangenome</a>
<ul>
<li><a href="#org436ee36">4.1. Pangenome GFA format</a></li>
<li><a href="#org6cd667b">4.2. Pangenome in ODGI format</a></li>
<li><a href="#org220b6cb">4.3. Pangenome RDF format</a></li>
<li><a href="#org78f267a">4.4. Pangenome Browser format</a></li>
</ul>
</li>
<li><a href="#org8cced34">5. Log of workflow output</a></li>
<li><a href="#org9d23c51">6. All files</a></li>
<li><a href="#org105d2d4">7. Planned</a>
<ul>
<li><a href="#org52bb570">7.1. Raw sequence data</a></li>
<li><a href="#org68c178c">7.2. Multiple Sequence Alignment (MSA)</a></li>
<li><a href="#org9ccf15c">7.3. Phylogenetic tree</a></li>
<li><a href="#org31c2b68">7.4. Protein prediction</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgcde4e6b" class="outline-2">
<h2 id="orgcde4e6b"><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-org1b46d7e" class="outline-2">
<h2 id="org1b46d7e"><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-orgf2db570" class="outline-2">
<h2 id="orgf2db570"><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
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-org9f89b24" class="outline-2">
<h2 id="org9f89b24"><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-org436ee36" class="outline-3">
<h3 id="org436ee36"><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-org6cd667b" class="outline-3">
<h3 id="org6cd667b"><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-org220b6cb" class="outline-3">
<h3 id="org220b6cb"><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-org78f267a" class="outline-3">
<h3 id="org78f267a"><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-org8cced34" class="outline-2">
<h2 id="org8cced34"><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-org9d23c51" class="outline-2">
<h2 id="org9d23c51"><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-org105d2d4" class="outline-2">
<h2 id="org105d2d4"><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-org52bb570" class="outline-3">
<h3 id="org52bb570"><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-org68c178c" class="outline-3">
<h3 id="org68c178c"><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-org9ccf15c" class="outline-3">
<h3 id="org9ccf15c"><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-org31c2b68" class="outline-3">
<h3 id="org31c2b68"><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>
<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 2020-05-30 Sat 10:40</small>.
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