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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/blends-team/med/-/commit/7f701a7887668ca02be45e41b594adda487551d8">7f701a78</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-04T21:04:54+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add links to software mentioned in paper at https://www.preprints.org/manuscript/202005.0376/v1
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<h4>1 changed file:</h4>
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+
covid-19_doc/Computational_Strategies_to_Combat_COVID-19.txt
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<h4>Changes:</h4>
<li id="70223b82cafb5fd5ad492f50fd47d79922bdc9b4">
<a href="https://salsa.debian.org/blends-team/med/-/commit/7f701a7887668ca02be45e41b594adda487551d8#70223b82cafb5fd5ad492f50fd47d79922bdc9b4"><strong>covid-19_doc/Computational_Strategies_to_Combat_COVID-19.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">https://www.preprints.org/manuscript/202005.0376/v1</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Computational strategies to combat COVID-19: Useful tools</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">to accelerate SARS-CoV-2 and Coronavirus research</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Detection and annotation</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">========================</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">PriSeTi https://github.com/mariehoffmann/PriSeT</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">CoVPipe https://gitlab.com/RKIBioinformaticsPipelines/</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ncov_minipipe https://github.com/replikation/poreCov</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">VADR https://github.com/nawrockie/vadr</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">V-Pipe https://github.com/cbg-ethz/V-pipe</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Haploflow https://nextcloud.bifo.helmholtz-hzi.de/s/j4MyspJs5kfdZxy</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">VIRify https://github.com/EBI-Metagenomics/emg-viral-pipeline</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">VBRC genome analysis tools https://www.4virology.net</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">VIRULIGN https://github.com/rega-cev/virulign</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Rfam COVID-19 https://rfam.org/covid-19</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">UniProt COVID-19 https://covid-19.uniprot.org/</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Pfam https://pfam.xfam.org</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Tracking, epidemiology and evolution</span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">====================================</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Covidex https://sourceforge.net/projects/covidex</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Pangolin https://github.com/hCoV-2019/pangolin/</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">BEAST2 https://www.beast2.org/</span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Phylogeographic reconstruction https://github.com/hzi-bifo/Phylogeography_Paper</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">COPASI https://github.com/copasi</span>
</pre>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">COVIDSIM http://www.kaderali.org:3838/covidsim</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">CoV-GLUE http://cov-glue.cvr.gla.ac.uk/</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">PoSeiDon https://github.com/hoelzer/poseidon</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Drug design</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">===========</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">VirHostNet http://virhostnet.prabi.fr/</span>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">CORDITE https://cordite.mathematik.uni-marburg.de</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">CoVex https://exbio.wzw.tum.de/covex/</span>
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">P-HIPSTer http://www.phipster.org/</span></pre>
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