<p>Hello.</p>

<p>I was working on a pipeline for genome assembly and I have used the human paired-end NGS data.</p>

<p>I want to compare my denovo assembly to the available human genome which is based on Sanger sequencing mainly.
How can I compare my denovo assembly to the sanger sequencing inorder to check -</p>

<ol>
<li><p>How much of the genome was covered in the denovo assembly?</p></li>
<li><p>How many regions of the genome have I missed in the denovo contigs?</p></li>
<li><p>Do I compare the contigs or scaffolds to the reference which is ordered as chromosomes?</p></li>
</ol>

<p>I know Quast is used to test different genome assembly qualities, but what about comparing a denovo assembly to a reference genome???</p>

<p>Quast also works with a reference genome, just set the reference with <code>-R</code>.  According to their <a href='http://quast.bioinf.spbau.ru/manual.html'>manual</a>, Quast has tests that will give you answers to points 1 &amp; 2. As for point 3, Quast has a <code>--scaffolds</code> option which, if given scaffolds will break them back into contigs.  You could run it with and without the <code>--scaffolds</code> option to see the difference in the metrics. There is also <a href='http://www.ncbi.nlm.nih.gov/pubmed/23303509'>ALE</a> for looking at assembly metrics although I'm not very familiar with it</p>
