Stats on assembly

AdrianP · 09-12-2013, 05:37 PM

Hello,

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:

Code:

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

luc · 09-12-2013, 06:03 PM

The assemblathon_stats.pl script from here is what I am using:
https://github.com/ucdavis-bioinform...thon2-analysis

It requires the FAlite.pm module from the same page.

maasha · 09-13-2013, 12:56 AM

You can use Biopieces (www.biopieces.org):

https://code.google.com/p/biopieces/...embled_contigs

flxlex · 09-13-2013, 02:09 AM

Or Quast (even without a reference): http://quast.bioinf.spbau.ru/

Blahah404 · 09-13-2013, 03:53 AM

leaff --stats is also nice, and very fast.

krobison · 09-13-2013, 06:04 AM

You show a pretty mongo Perl one-liner but "aren't good at scripting"? Perhaps you are selling yourself short.

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09-12-2013, 05:37 PM	#1
AdrianP Senior Member Location: Ottawa Join Date: Apr 2011 Posts: 130	Stats on assembly Hello, 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: Code: 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

09-12-2013, 06:03 PM	#2
luc Senior Member Location: US Join Date: Dec 2010 Posts: 452	The assemblathon_stats.pl script from here is what I am using: https://github.com/ucdavis-bioinform...thon2-analysis It requires the FAlite.pm module from the same page.

09-13-2013, 12:56 AM	#3
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	You can use Biopieces (www.biopieces.org): https://code.google.com/p/biopieces/...embled_contigs

09-13-2013, 02:09 AM	#4
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	Or Quast (even without a reference): http://quast.bioinf.spbau.ru/

09-13-2013, 03:53 AM	#5
Blahah404 Member Location: Cambridge, UK Join Date: Dec 2011 Posts: 48	leaff --stats is also nice, and very fast.

09-13-2013, 06:04 AM	#6
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	You show a pretty mongo Perl one-liner but "aren't good at scripting"? Perhaps you are selling yourself short.