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	<title><![CDATA[BOL: January 2019]]></title>
	<link>https://bioinformaticsonline.com/blog/archive/biostar/1546322400/1549000800?</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly</guid>
	<pubDate>Tue, 22 Jan 2019 09:39:02 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly</link>
	<title><![CDATA[List of tools frequently used while genome assembly]]></title>
	<description><![CDATA[<h4>List of tools frequently used while genome assembly:</h4><p>I have used the following assemblers</p><ul>
<li><a href="http://bioinf.spbau.ru/spades">Spades</a>&nbsp;(v. 3.10.1)</li>
<li><a href="http://canu.readthedocs.io/en/stable/index.html">CANU</a>&nbsp;(v. 1.6)</li>
<li><a href="https://github.com/rrwick/Unicycler">Unicycler&nbsp;</a>(v. v0.4.1)</li>
<li><a href="https://github.com/lh3/miniasm">Miniasm</a>&nbsp;(v. 0.2-r137-dirty)</li>
</ul><p>I have used the following mappers</p><ul>
<li><a href="https://github.com/lh3/minimap2">minimap2</a>&nbsp;(v.&nbsp;2.0rc1-r232)</li>
<li><a href="https://github.com/lh3/minimap">minimap&nbsp;</a>(v. 0.2-r124-dirty)</li>
<li><a href="https://github.com/lh3/bwa">bwa</a>&nbsp;(v.&nbsp;0.7.12-r1039)</li>
</ul><p>I have used the following polishing tools</p><ul>
<li><a href="https://github.com/isovic/racon">Racon</a>&nbsp;(v. not available)</li>
<li><a href="https://github.com/broadinstitute/pilon">Pilon</a>&nbsp;(v. 1.18)</li>
<li><a href="https://github.com/jts/nanopolish">Nanopolish</a>&nbsp;(v. 0.8.3)</li>
</ul><p>I have used the following tools to assess genome assembly characteristics</p><ul>
<li><a href="https://github.com/chjp/ANI">ANI.pl</a>&nbsp;(https://github.com/chjp/ANI)</li>
<li><a href="http://ecogenomics.github.io/CheckM/">CheckM</a>&nbsp;(v. 1.0.7)</li>
<li><a href="https://github.com/tseemann/prokka">Prokka</a>&nbsp;(v. 1.12)</li>
<li><a href="http://bioinf.spbau.ru/en/quast">QUAST</a>&nbsp;(v. 2.3)</li>
<li><a href="http://mummer.sourceforge.net/">mummer&nbsp;</a>(v. not available)</li>
</ul><p>If you have any ideas or superior tools we have missed please let us know in the comments.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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