<p>I often see the word <strong>depth</strong> in the manuals of the tools for NGS, what is its meaning  ?</p>

<p>thanks.</p>

<p>Eric gives the correct answer for depth (of coverage). I think confusion in this area stems not from the term "depth" but from the term "coverage".  Coverage now appears to have 3 meanings:</p>

<ol>
<li>the theoretical "fold-coverage"
of a shotgun sequencing experiment:
number of reads * read length /
target size </li>
<li>the theoretical or
empirical "breadth-of-coverage" of
an assembly: assembly size / target
size</li>
<li>the empirical average
"depth-of-coverage" of an assembly:
number of reads * read length /
assembly size</li>
</ol>

<p>(1) and (3) are not the same because of sequencing error &amp; unclonable/unmappable regions of the genome. <a href='http://en.wikipedia.org/wiki/DNA_sequencing_theory#Lander-Waterman_theory'>Lander-Waterman theory</a> deals with the relationship between (1) and (2).</p>
