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<!DOCTYPE html>
<html>
{% include 'header.html' %}
{% include 'mapheader.html' %}
<body>
{% include 'banner.html' %}
{% include 'menu.html' %}
<section>
<div class="intro">
<p>
COVID-19 PubSeq is a free and open online
bioinformatics public sequence resource with
on-the-fly analysis of sequenced SARS-CoV-2
samples that allows for a quick turnaround in
identification of new virus strains. PubSeq allows
anyone to upload sequence material in the form of
FASTA or FASTQ files with accompanying metadata
through the <a href="/upload">web interface</a> or <a href="/apidoc">REST API</a>.
</p>
<p>
Make your sequence
data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
your SARS-CoV-2 sequence (FASTA or FASTQ formats)
with simple metadata (JSONLD) to
the <a href="/about">public sequence
resource</a>. The upload will trigger a recompute
with all available sequences into a Pangenome
available for
<a href="/download">download</a>!
</p>
<p>
Your uploaded sequence will automatically be
processed and incorporated into the public
pangenome with metadata using worklows from the
High Performance Open Biology Lab
defined <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All
data is published under
a <a href="https://creativecommons.org/licenses/by/4.0/">Creative
Commons license</a> You can take the published
(GFA/RDF/FASTA) data and store it in a triple
store for further processing. Clinical data can
be stored securely
at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
</p>
<p>
Note that form fields contain
web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
URI's</a>
for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
and machine readable metadata. For examples of
use, see the <a href="/blog">BLOG</a>.
</p>
</div>
</section>
<section id="map_view" class="map">
<div id="mapid"></div>
</section>
{% include 'footer.html' %}
<script type="text/javascript">
let scriptRoot = {{ request.script_root|tojson|safe }}; // examples
drawMap()
</script>
</body>
</html>
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