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Old 10-20-2016, 08:57 AM   #1
SDPA_Pet
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Default Bbtools/BBmaps output questions

Hello, I am using "stats.sh" command in BBtools to check my assembled metagenomes. I am looking for N50 and the largest contig. In my case, there is a line shows "Main genome contig N/L50: 7688/759" and "Max contig length: 5.905 KB". I know N50 and L50? What is N/L50 here? Does this mean N50 = 7688 and L50=759? Why my max contig length is shorter than N50? Is this possbile? (details see attached files)

A C G T N IUPAC Other GC GC_stdev
0.2126 0.2873 0.2874 0.2127 0.0000 0.0000 0.0000 0.5747 0.0976

Main genome scaffold total: 19074
Main genome contig total: 19074
Main genome scaffold sequence total: 15.193 MB
Main genome contig sequence total: 15.193 MB 0.000% gap
Main genome scaffold N/L50: 7688/759
Main genome contig N/L50: 7688/759
Main genome scaffold N/L90: 16532/636
Main genome contig N/L90: 16532/636
Max scaffold length: 5.905 KB
Max contig length: 5.905 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB: 0.00%
Attached Files
File Type: txt output.txt (1.5 KB, 2 views)
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Old 10-21-2016, 04:32 AM   #2
kmcarr
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Default

Quote:
Originally Posted by SDPA_Pet View Post
Does this mean N50 = 7688 and L50=759?
Yes, that is what that means.
Quote:
Why my max contig length is shorter than N50? Is this possbile?
Because Brian believes (and I agree with him, not that he requires any validation from me) the proper notation should be N50=number of contigs making 50% of your assembly and L50=length lower limit of contigs making up 50% of your assembly. So what stats.sh is telling you is that the largest 7,688 contigs account for 50% of your assembly length and those contigs are all ≥ 759bp.
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