[Bioperl-l] reverse complement of fastq

Fields, Christopher J cjfields at illinois.edu
Thu Aug 30 14:54:14 EDT 2012


If you want something that gives you revcom *very quickly*, Bioperl is sadly not the way to go just yet.  However, you can use something like seqtk, which is very fast:

    https://github.com/lh3/seqtk

Something like this should work:

$ seqtk seq -r orig.fq > rc.fq

chris

On Aug 30, 2012, at 1:07 PM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> HI,
>     I have a fastq file with few million reads. I need to find reverse
> complement of the reads.
> I used 'revcom' method but its not working for fastq.
> 
> I will really appreciate if anyone can help me out.
> 
> Thanks
> Shalabh
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list