Can anyone tell me the difference between N50 and L50 when using in genome assembly.
Tank you!
Tank you!
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There are different definitions...Originally posted by moolder View Post
Nature Reviews Genetics 13, 329-342 (May 2012) | doi:10.1038/nrg3174
A beginner's guide to eukaryotic genome annotation
Mark Yandel1 & Daniel Ence
Another (I guess more welcomed?) definition would be:Genome assemblies are composed of scaffolds and contigs. Contigs are contiguous consensus sequences that are derived from collections of overlapping reads. Scaffolds are ordered and orientated sets of contigs that are linked to one another by mate pairs of sequencing reads.
Scaffold and contig N50s
By far the most widely used statistics for describing the quality of a genome assembly are its scaffold and contig N50s. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. The scaffold N50 is calculated in the same fashion but uses scaffolds rather than contigs. The longer the scaffold N50 is, the better the assembly is. However, it is important to keep in mind that a poor assembly that has forced unrelated reads and contigs into scaffolds can have an erroneously large N50. Note too that scaffolds and contigs that comprise only a single read or read pair — often termed 'singletons' — are frequently excluded from these calculations, as are contigs and scaffolds that are shorter than ~800 bp. The procedures used to calculate N50 may therefore vary between genome projects.
Percent gaps
Another important assembly statistic is its percent gaps.Unsequenced regions between mate pairs in contigs and between scaffolds are often represented as runs of 'N's in the final assembly. Thus two assemblies can have identical scaffold N50s but can still differ in their percent gaps: one has very few gaps, and the other is heavily peppered with them. Estimates of gap lengths are often made based on library insert sizes and read lengths; when these are available, the number of 'N's in these gaps usually, but not always, represents the most likely estimate of that gap's size; sometimes, all gaps are simply represented by a run of 50 'N's regardless of their size.
N50 is the number of contigs (sorted by length from longest to shortest) whose length when summed up covers 50% or more of the genome assembly. Let's say your total assembly length is 10mb and you have 5 contigs/scaffolds of length 5mb, 4mb, 3mb, 2mb and 1mb. If you want the N50 you sort the contigs/scaffolds by length and sum them up until you cover 50% or more of the assembly, that would be 5mb + 4mb = 9mb which is 60%. The N50 would then be 2, because you need just 2 contigs/scaffolds to cover 50% or more of the assembly. The L50 would be the length of the smallest contig/scaffold in the N50 set, i.e. the length of the last contig/scaffold added to cover 50% or more of the assembly. Therefore, the L50 of this example would be the contig/scaffold length of 4mb.
Both metrics can be applied to assemblies with just contigs or scaffolded contigs. If you have scaffolds and want contig metrics, you need to partition each scaffold into contigs again by breaking them up where the NNNN junctions occur.Last edited by Guest; 03-28-2013, 03:35 AM. -
WARNING!!!!
The post above has L50 and N50 reversed. I'm very concerned that people will be misled.
Please consult other sources for N50 and L50!Comment
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How is it reversed if I mentioned two different explanations - the first source I quoted explains N50 length and the other source explains N50 as count and L50 as length? Both cases are covered.Originally posted by dgordon View Post
There's an entire discussion on this, which explanation is right:
and people are clearly divided.
Even if there was (but there really isn't) a consensus that N50 indicates length and L50 count, go look at genome assembly reports and papers and you will still find it "the other way round" from what you also think is right:
Scaffold N50 (L50) = 51 (993 Kbp)
Contig N50 (L50) = 1476 (37.6 Kbp)
For the scaffolds the N50 is 5 and the L50 is 57.5Mb;
Please consult literature before correcting someone with your subjective opinion.
The best way to go about this, whether you're using N50 or L50 for one or the other is to be more descriptive like by including "???50 scaffold length" and "???L50 scaffold count". Whether you prefer N or L in that case everybody will understand what you're referring to.Last edited by Guest; 09-25-2015, 07:43 AM.Comment
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