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[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;">Bambus2 is a scaffolding module that can be applicable to metagenomics settings. MetaVelvet uses a novel graph splitting algorithm during contiging process, and uses the scaffolding module of Velvet (RockBand and Pebble) during scaffolding process. Alternatively, users can output MetaVelvet contigs and uses Bambus2 scaffolding module instead of using RockBand and Pebble.</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 /><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? </li>
<li><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 <br /><br /></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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