[Bioperl-l] unambiguous assembly of fastq reads into fastq sequences combining q-scores

Sean Davis sdavis2 at mail.nih.gov
Wed Mar 10 05:31:50 EST 2010

On Wed, Mar 10, 2010 at 3:55 AM, Albert Vilella <avilella at gmail.com> wrote:
> Hi all,
> I would like to know if anyone knows of a script or method in bioperl
> to do an unambiguous assembly of fastq sequences, combining the q-scores to
> give assembled fastq sequences as the output.
> By unambiguous I mean something like what abyss would produce with this options:
> ABYSS -k$k -b0 -t0 -e0 -c0
> but giving assembled fastq sequences with combined q-scores as output
> instead of simple
> fasta assembled sequences.

Hi, Albert.

I'm not sure exactly what you want here, but have you looked at the
Mosaik aligner?  Also, look at samtools pileup; you can probably
produce something similar to what you want from it as well.

I certainly might have misunderstood the problem, though.


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