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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="#org42addaa">1. FASTA files</a></li>
<li><a href="#org04bd8c7">2. Metadata</a></li>
<li><a href="#orgead2f03">3. Pangenome</a>
<ul>
<li><a href="#org8ea7d40">3.1. Pangenome GFA format</a></li>
<li><a href="#orge7808d6">3.2. Pangenome in ODGI format</a></li>
<li><a href="#orgaadcde8">3.3. Pangenome RDF format</a></li>
<li><a href="#orga3a0408">3.4. Pangenome Browser format</a></li>
</ul>
</li>
<li><a href="#org1bbb7e6">4. Log of workflow output</a></li>
<li><a href="#orgd16b2c8">5. All files</a></li>
<li><a href="#org9d40ed2">6. Planned</a>
<ul>
<li><a href="#org70cb9d5">6.1. Raw sequence data</a></li>
<li><a href="#org38cfa2e">6.2. Multiple Sequence Alignment (MSA)</a></li>
<li><a href="#org507c7dd">6.3. Phylogenetic tree</a></li>
<li><a href="#orgca26edf">6.4. Protein prediction</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org42addaa" class="outline-2">
<h2 id="org42addaa"><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-org04bd8c7" class="outline-2">
<h2 id="org04bd8c7"><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-orgead2f03" class="outline-2">
<h2 id="orgead2f03"><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-org8ea7d40" class="outline-3">
<h3 id="org8ea7d40"><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-orge7808d6" class="outline-3">
<h3 id="orge7808d6"><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 optimised dynamic genome/graph
implementation.
</p>
</div>
</div>
<div id="outline-container-orgaadcde8" class="outline-3">
<h3 id="orgaadcde8"><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-orga3a0408" class="outline-3">
<h3 id="orga3a0408"><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-org1bbb7e6" class="outline-2">
<h2 id="org1bbb7e6"><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-orgd16b2c8" class="outline-2">
<h2 id="orgd16b2c8"><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 id="outline-container-org9d40ed2" class="outline-2">
<h2 id="org9d40ed2"><span class="section-number-2">6</span> Planned</h2>
<div class="outline-text-2" id="text-6">
<p>
We are planning the add the following output (see also
</p>
</div>
<div id="outline-container-org70cb9d5" class="outline-3">
<h3 id="org70cb9d5"><span class="section-number-3">6.1</span> Raw sequence data</h3>
<div class="outline-text-3" id="text-6-1">
<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-org38cfa2e" class="outline-3">
<h3 id="org38cfa2e"><span class="section-number-3">6.2</span> Multiple Sequence Alignment (MSA)</h3>
<div class="outline-text-3" id="text-6-2">
<p>
See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>.
</p>
</div>
</div>
<div id="outline-container-org507c7dd" class="outline-3">
<h3 id="org507c7dd"><span class="section-number-3">6.3</span> Phylogenetic tree</h3>
<div class="outline-text-3" id="text-6-3">
<p>
See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>.
</p>
</div>
</div>
<div id="outline-container-orgca26edf" class="outline-3">
<h3 id="orgca26edf"><span class="section-number-3">6.4</span> Protein prediction</h3>
<div class="outline-text-3" id="text-6-4">
<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 2020-05-24 Sun 11:29</small>.
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