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What Does The "N50" Mean?

Hi Guys,

We often read in NGS papers a descriptive value, called "N50", which seems to provide a standard measure of assembly connectivity. Could someone please explain, in details, the meaning of "N50" and how to compute this value?

Regards

assembly
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updated by Ram Ram • written by Bioch'Ti • Bioch'Ti

3 answers

http://seqanswers.com/forums/showthread.php?t=2332

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updated by Ram Ram • written by Yannick Wurm Yannick Wurm

Of course, N50, being a single number and an internal measure (using only information from the assembly itself, no external reference), is not very informative. I'm using a graphical display of the assemblies - still an internal measure (although you can also use e.g. EST data to use it as an external control). Some examples here.

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updated by Ram Ram • written by Ketil Ketil

http://jermdemo.blogspot.com/2008/11/calculating-n50-from-velvet-output.html

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updated by Ram Ram • written by Jeremy Leipzig Jeremy Leipzig

I don't mean to bring up and old issue. I just need to clear up some confusion. Ultimately, for a good assembly, I want a fewer number of contigs, but I want the contigs to be larger. So, does that imply that I want L50 or N50 length to be large (relative to what's being sequenced)? and I also want N50 to be large as well?

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written by diltsjeri diltsjeri

you want L50 to be large and N50 to be small, so you wouldn't need many contigs to cover most of the assembly

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written by Jeremy Leipzig Jeremy Leipzig

great! thanks for responding. It makes perfect sense.

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written by diltsjeri diltsjeri

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