What Does The "N50" Mean?
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11.5 years ago
Bioch'Ti ★ 1.0k

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 • 22k views
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Thanks Yannick!

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10.9 years ago
Ketil 4.1k

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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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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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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great! thanks for responding. It makes perfect sense.

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