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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 <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2&sort=date">SARS-CoV-2</a>
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>. For more
information see the <a href="/about">FAQ!</a>.
</p>
<section class="flex-container">
<div id="map_view" class="map">
<div id="mapid"></div>
</div>
<div id="feed">
<input name="feed-tabs" type="radio" id="tab-all-items" checked/>
<label for="tab-all-items">All Items</label>
<input name="feed-tabs" type="radio" id="tab-arxiv-articles"/>
<label for="tab-arxiv-articles">Arxiv</label>
<input name="feed-tabs" type="radio" id="tab-pubmed-articles"/>
<label for="tab-pubmed-articles">Pubmed</label>
<input name="feed-tabs" type="radio" id="tab-tweets"/>
<label for="tab-tweets">Tweets</label>
<input name="feed-tabs" type="radio" id="tab-commits"/>
<label for="tab-commits">Commits</label>
<ul class="tab content-all-items">
<!-- Begin News -->
{% if all_items %}
{% for item in all_items|sort(reverse=true, attribute="score")%}
<li>
{% if item['authors'] %}
<!-- Arxiv article -->
<p>
<b>[arxiv]</b>
<a href="{{ item['url'] }}" target="_blank">
{{item['title']}}
</a>
<br/>
<b>Authors:</b> {{ item['authors'] }}
<br/>
<b>Abstract:</b> {{ item['abstract']}}...
<br/>
<b>Submitted:</b> {{ item['submission']}}
</p>
{% elif item['full-authors'] %}
<!-- Pubmed Article -->
<p><b>[Pubmed]:</b>
<a href="https://pubmed.ncbi.nlm.nih.gov/{{ item['docsum-pmid'] }}" target="_blank"><b>Summary:</b>
{{ item['summary'] }}
</a> <br/>
<b>Full Authors:</b> {{ item['full-authors'] }} <br/>
<b>Short Authors:</b> {{ item['short-authors'] }} <br/>
<b>Citation:</b> {{ item['citation'] }} <br/>
<b>Short Journal Citation:</b> {{ item['short-journal-citation'] }} <br/>
</p>
{% elif item['tweet'] %}
<!-- Tweets -->
<p>
<b>[Tweet]:</b>
{{ item['tweet']|urlize(40, target="_blank")}}
<small>
<a href="{{ item['url'] }}" target="_blank">source</a></small>
<br/>
by {{ item['author'] }}
<br/>
<small>{{ item['timeposted'] }}</small>
</p>
{% elif item['repository-url'] %}
<!-- Commits -->
<p>
<b>[Commit]:</b>
<a href="{{ item.url }}" target="_blank">
{{ item.hash.split(":")[-1][:7] }}: {{ item.content }}
</a>
<br/>
<small>
<a href="{{ item['repository-url'] }}" target="_blank"> {{ item.author }}/{{ item.repository }}</a>
on {{ item.timeposted }}
</small>
</p>
{% endif %}
</li>
{%endfor%}
{% else %}
There are no items to display :(
{% endif %}
<!-- End News -->
</ul>
<ul class="tab content-arxiv-articles">
{% if arxiv_articles %}
{% for article in arxiv_articles|sort(reverse=true, attribute="score")%}
<li>
<p><a href="{{article['url']}}">{{ article['title'] }}</a></p>
<p><b>Authors:</b> {{ article['authors'] }}</p>
<p><b>Abstract:</b> {{ article['abstract']}}...</p>
<p><b>Submitted:</b> {{ article['submission']}}</p>
</li>
{% endfor %}
{% else %}
There are no articles to display :(
{% endif %}
</ul>
<ul class="tab content-pubmed-articles">
{% if pubmed_articles %}
{% for article in pubmed_articles|sort(reverse=true, attribute="score")%}
<li>
<p><a href="https://pubmed.ncbi.nlm.nih.gov/{{article['docsum-pmid']}}"><b>Summary:</b> {{ article['summary'] }}</a></p>
<p><b>Full Authors:</b> {{ article['full-authors'] }}</p>
<p><b>Short Authors:</b> {{ article['short-authors'] }}</p>
<p><b>Citation:</b> {{ article['citation'] }}</p>
<p><b>Short Journal Citation:</b> {{ article['short-journal-citation'] }}</p>
</li>
{% endfor %}
{% else %}
There are no articles to display :(
{% endif %}
</ul>
<ul class="tab content-tweets">
{% if tweets %}
{% for tweet in tweets|sort(reverse=true, attribute="score")%}
<li>
<p class="tweet">
{{ tweet.tweet|urlize(40, target="_blank") }} <br/>
by {{ tweet.author }}
</p>
<small class="timeposted">
{{ tweet.timeposted }}
</small>
</li>
{% endfor %}
{% else %}
There are no tweets to display :(
{% endif %}
</ul>
<ul class="tab content-commits">
{% if commits %}
{% for commit in commits|sort(reverse=true, attribute="score")%}
<li>
<p class="commit">
<a href="{{commit.url}}" target="_blank">
{{ commit.hash.split(":")[-1][:7] }}:{{ commit.content}}
</a>
</p>
<small class="timeposted">
<a href="{{ commit['repository-url']}}" target="_blank">{{ commit.author }}/{{ commit.repository }}</a>
on {{ commit.timeposted}}
</small>
</li>
{% endfor %}
{% else %}
There are no commits to be displayed.
{% endif %}
</ul>
</div>
</section>
<a href="https://projectredcap.org/"><img class="img-right" src="static/image/REDCap.png" /></a>
<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>
<a href="https://nanoporetech.com/"><img class="img-right" src="static/image/oxford-nanopore2.jpg" /></a>
<p>
Data can be uploaded from any sequencing platform
in FASTA format. We give special attention to
workflows for
the <a href="https://nanoporetech.com/">Oxford
Nanopore</a> - see
also <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2+nanopore&sort=date">pubmed</a>
- because it offers an affordable platform that is
great for SARS-CoV-2 sequencing and
identification. In New Zealand the Oxford Nanopore
is used for all
<a href="https://www.esr.cri.nz/home/about-esr/media-releases/esr-performs-first-new-zealand-genome-sequencing-on-covid-19-sample/">tracing</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">docs</a>.
</p>
</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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