Question: What Does The "N50" Mean?
6
gravatar for Bioch'Ti
8.8 years ago by
Bioch'Ti1000
France (Avignon)
Bioch'Ti1000 wrote:

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 • 19k views
ADD COMMENTlink modified 8.1 years ago by Ketil3.9k • written 8.8 years ago by Bioch'Ti1000
8
gravatar for Yannick Wurm
8.8 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

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

ADD COMMENTlink written 8.8 years ago by Yannick Wurm2.3k

Thanks Yannick!

ADD REPLYlink written 8.8 years ago by Bioch'Ti1000
5
gravatar for Ketil
8.3 years ago by
Ketil3.9k
Germany
Ketil3.9k wrote:

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 at http://blog.malde.org/index.php/a50-a-graphical-comparison-of-genome-assemblies/

ADD COMMENTlink written 8.3 years ago by Ketil3.9k
2
gravatar for Jeremy Leipzig
8.8 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

ADD COMMENTlink modified 6.1 years ago • written 8.8 years ago by Jeremy Leipzig18k

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?

ADD REPLYlink written 6.7 years ago by diltsjeri420
1

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

ADD REPLYlink written 6.7 years ago by Jeremy Leipzig18k

great! thanks for responding. It makes perfect sense.

ADD REPLYlink written 6.7 years ago by diltsjeri420
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