SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
Quick question about Bowtie -m biznatch Bioinformatics 0 09-26-2012 06:29 PM
Quick guide materials for a freshman liu_xt005 General 1 06-14-2011 05:55 PM
quick seq format question swarbre Bioinformatics 0 03-23-2011 01:41 AM
BFAST- match quick question newbietonextgen Bioinformatics 9 11-23-2010 01:39 PM
Quick and dirty? scientifica Bioinformatics 5 01-27-2010 11:53 PM

Closed Thread
 
Thread Tools
Old 09-12-2013, 06:37 AM   #1
AdrianP
Senior Member
 
Location: Ottawa

Join Date: Apr 2011
Posts: 130
Default Quick Evaluator of Denovo Assemblies

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
AdrianP is offline  
Old 09-13-2013, 01:10 AM   #2
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

Double posting in Bioinformatics thread - where you are getting relevant answers: http://seqanswers.com/forums/showthread.php?t=33684
flxlex is offline  
Closed Thread

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:23 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO