[Bioperl-l] Trimming low quality reads

[Chris Fields]

+1 on using fastx.  I believe this is what our local seq pipeline uses prior to us sending out the processed stuff.

chris

On Feb 16, 2011, at 10:41 AM, Jason Stajich wrote:

> I would use a faster implementation like the fastx toolkit - http://hannonlab.cshl.edu/fastx_toolkit/
> 
> There are lots of answers to NGS questions on seqanswers too
> http://www.google.com/search?q=site:seqanswers.com+trim
> 
> 
> Jordi Durban wrote:
>> Well, there's a program called Seqtrim that uses bioperl to trim the
>> sequences.
>> Here more information:
>> http://www.scbi.uma.es/cgi-bin/seqtrim/seqtrim_login.cgi
>> Hope this helps.
>> 
>> 2011/2/16 shalabh sharma<shalabh.sharma7 at gmail.com>
>> 
>>> Hi,
>>>    Is there any bioperl module available to quality trim in fasta-qual
>>>  format.
>>> i am little worried about the efficiency as i have huge data (~ 50 gb).
>>> Also i would really appreciate if some one has some other suggestions.
>>> 
>>> Thanks
>>> Shalabh
>>> _______________________________________________
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>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
>> 
> 
> -- 
> Jason Stajich
> 
> 
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