<p>I understand the meaning of N50 contig <em>length</em>, but lately I've been coming across assembly statistics that report the N50 contig <em>number</em>. Can someone explain what is meant by N50 contig number and how it relates to assembly quality?</p>

<p>N50-length is the length of that last contig that puts you over the top.
 N50-contig number (i.e. N50) is just the rank of that contig.</p>
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<p>91 77 70 69 62 56 45 29 16 4[?]N50 vs N50 length[?]
Technically N50, as opposed to N50 length, refers to the ordinal of that last contig that pushes it over the brink - in this example 4 (since 69bp is the 4th largest contig). Unfortunately, a higher N50 implies the opposite of a longer N50 length. Some papers refer to N50 length as L50, while most have simply followed the lazy convention of dropping "length" off of "N50 length". I think it is important to include units with your N50 to minimize confusion.</p>
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<p><a href="http://jermdemo.blogspot.com/2008/11/calculating-n50-from-velvet-output.html">http://jermdemo.blogspot.com/2008/11/calculating-n50-from-velvet-output.html</a></p>