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Old 09-12-2013, 05:37 PM   #1
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Location: Ottawa

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Default Stats on assembly


I was wonder if there is, or if it is possible to make a script that would quickly evaluate a given fasta file with contigs.

Something that VelvetOptimiser spits out:

Total number of contigs: 49644
n50: 546
length of longest contig: 21951
Total bases in contigs: 25417931
Number of contigs > 1k: 3773
Total bases in contigs > 1k: 6821103

I know you can get the n50 from a simple perl script:
perl -e 'my ($len,$total)=(0,0);my @x;while(<>){if(/^[\>\@]/){if($len>0){$total+=$len;push@x,$len;};$len=0;}else{s/\s//g;$len+=length($_);}}if ($len>0){$total+=$len;push @x,$len;}@x=sort{$b<=>$a}@x; my ($count,$half)=(0,0);for (my $j=0;$j<@x;$j++){$count+=$x[$j];if(($count>=$total/2)&&($half==0)){print "N50: $x[$j]\n";$half=$x[$j]}elsif($count>=$total*0.9){print "N90: $x[$j]\n";exit;}}' CONTIGS.fasta
Anyone have any idea if such a thing exists? I am not a big scripter myself so I can't help myself now
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Old 09-12-2013, 06:03 PM   #2
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The script from here is what I am using:

It requires the module from the same page.
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Old 09-13-2013, 12:56 AM   #3
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You can use Biopieces (
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Old 09-13-2013, 02:09 AM   #4
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Or Quast (even without a reference):
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Old 09-13-2013, 03:53 AM   #5
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leaff --stats is also nice, and very fast.
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Old 09-13-2013, 06:04 AM   #6
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You show a pretty mongo Perl one-liner but "aren't good at scripting"? Perhaps you are selling yourself short.
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