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[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Contrary to single-genome assemblers (e.g., Velvet and SOAPdenovo), MetaVelvet assumes metagenomics settings. Accordingly, </span><em style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">k</em><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">-mer coverage histogram might be multi-modal rather than uni-modal. Please note that the coverage peak parameters can largely affect MetaVelvet assembling results. Although simple and automatic peak detection algorithm is implemented in </span><strong style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">meta-velvetg</strong><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">, we strongly recommend manual inspection of </span><em style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">k</em><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">-mer coverage peaks and manual setting of the coverage peak parameters. For manually setting the coverage peak parameters, please execute the following procedures.</span>

[GUIDELINES]
For installation and getting started protocol click <a href="https://www.protocols.io/view/MetaVelvet-Installation-and-Getting-Started-d5k84v" target="_blank">here</a>. <br /><br /><strong style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Frequently Asked Questions<br /></strong>
<ul style="padding-left: 60px;">
<li><strong>Q:</strong> <strong>meta-velveth</strong> is not generated in the new version (&gt;= 1.1.01). Is it problem? <br /><strong>A:</strong> This is not problem. The usage of MetaVelvet is changed when the version 1.1.01 is released, and the new version does not include <strong>meta-velveth</strong>. Instead, please use <strong>velveth</strong>, <strong>velvetg</strong>, and <strong>meta-velvetg</strong>.</li>
</ul>
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<ul style="padding-left: 60px;">
<li><strong>Q:</strong> When only one coverage peak is detected (or manually input), is there any difference between MetaVelvet and Velvet algorithms? <br /><strong>A:</strong> There is no substantial difference. In such cases, <strong>meta-velvetg</strong> moves to "single-peak mode" and graph splitting functions in <strong>meta-velvetg</strong> is not called. Instead of graph splitting functions, standard velvet functions are called in such cases.</li>
</ul>
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<ul style="padding-left: 60px;">
<li><strong>Q:</strong> What's the difference in working procedures between <strong>velvetg</strong>, <strong>meta-velvetg</strong> (&lt;= 0.3.1), and <strong>meta-velvetg</strong>(&gt;= 1.1.01)? <br /><strong>A:</strong> The following is the working procedure of <strong>velvetg</strong>, <strong>meta-velvetg</strong> (&lt;= 0.3.1), and <strong>meta-velvetg</strong> (&gt;= 1.1.01): <br /><br />    <strong>velvetg &amp; meta-velvetg(&lt;=0.3.1) : </strong><br />        Load Sequences &amp; Roadmaps file <br />        -&gt; Generate PreGraph file <br />        -&gt; Generate Graph or Graph2 file <br />        -&gt; Generate contigs.fa and LastGraph <br /><br />    <strong>meta-velvetg (&gt;= 1.1.01): </strong><br />        Load Sequences &amp; Roadmaps &amp; Graph2 file <br />        -&gt; Generate meta-velvetg.contigs.fa and meta-velvetg.LastGraph </li>
</ul>
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<ul style="padding-left: 60px;">
<li><strong>Q:</strong> Is version compatibility between Velvet and MetaVelvet fully tested? <br /><strong>A:</strong> Version compatibility between Velvet-1.0.06 and MetaVelvet-1.1.01 is fully tested.</li>
</ul>
<br /><strong style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Troubleshooting<br /><br /></strong><strong style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Trouble:</strong><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">When drawing</span><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><em style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">k</em><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">-mer coverage histogram (as in the</span><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><a href="http://metavelvet.dna.bio.keio.ac.jp/MV.html#advanced-topic-1" target="_blank">"Advanced topics 1"</a><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">section), the following warning messages is appeared:</span>
<blockquote style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">&gt; weighted.hist(data$shot1_cov,data$lgth,breaks=seq(0,200,1)) <br />Warning messages: <br />1: In min(x, na.rm = na.rm) : <br />no non-missing arguments to min; returning Inf <br />2: In max(x, na.rm = na.rm) : <br />no non-missing arguments to max; returning -Inf <br />3: In weighted.hist(data$shot1_cov, data$lgth, breaks = seq(0, 200, : <br />Areas will not relate to frequencies </blockquote>
<strong style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Solution:</strong><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">This warning (error) is caused by "Inf" values in the Graph2 node stats. Accordingly, by removing "Inf" values from the Graph2 stats, the error is resolved:</span>
<blockquote style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">$ head -n 1 meta-velvetg.Graph2-stats.txt \ <br />        &gt; meta-velvetg.Graph2-stats.rmInf.txt <br />$ perl -ne '{print $_ unless /Inf/;}' \ <br />        meta-velvetg.Graph2-stats.txt \ <br />        &gt;&gt; meta-velvetg.Graph2-stats.rmInf.txt <br />$ R <br />&gt; library(plotrix) <br />&gt; data = read.table("meta-velvetg.Graph2-stats.rmInf.txt", header=TRUE) <br />&gt; weighted.hist(data$shot1_cov,data$lgth,breaks=seq(0,200,1)) </blockquote>
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[STEPS]
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