[Biopython-dev] sff reader

Peter biopython at maubp.freeserve.co.uk
Fri May 22 23:09:56 UTC 2009

On 5/22/09, Brad Chapman <chapmanb at 50mail.com> wrote:
> Peter and Jose;
>  I haven't used SFF files myself as we don't have a 454 machine,

We don't have one in house either, and have instead out-sourced to a
couple of sequencing centres in the UK with 454 machines.

>  but do know of a couple of implementations of SFF TO
>  Fastq/Fasta.
>  Flower is a Haskell implementation:
>  http://blog.malde.org/index.php/flower/
>  And PyroBayes is a 454 base caller:
>  http://bioinformatics.bc.edu/marthlab/PyroBayes
>  Depending on what you all end up doing, these might be useful as
>  comparison points, or for wrapping with Application command lines.

I would say Roche's own tools are the best reference, but these only
output FASTA and QUAL, not FASTQ files (at the moment at least). So
yes, being able to compare a Biopython SFF to FASTQ conversion with
that by Flower (or anything else) would be handy.


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