[Biopython] sff inot fasta and qual then trim

[Peter Cock]

On Tue, Oct 23, 2012 at 5:58 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
> Csaba,
>
> As Peter said, there are many packages which will convert sff to fastq/fasta.

Actually I meant trimming packages, although there are several SFF converters
as well e.g. Biopython, sff_extract, BioHaskell/Flower, and Roche's tools.

> I wonder if you're running into disk performance issues, rather than algorithm
> ones, though.  Using the BioPython SeqIO convert should tell you that much,
> though that does seem slow (at least for the systems that I work on).

Could be - disk IO will be a factor, but I suspect the quality
trimming to be the
slow part rather than the format conversion.

Peter