[Biopython-dev] sff reader

[Senthil Palanisami]

I have been working with SFF files for the past month, and can say it's
definitely frustrating working with custom binary formats.

Take a look at sff_extract which is written in python. It converts sff files
into fasta and xml or caf files:
http://bioinf.comav.upv.es/sff_extract/index.html

You can find detailed specs of the format @
http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#header-global


--
Senthil Palanisami
http://spenthil.com


On Fri, May 22, 2009 at 4:09 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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.
>
> Peter
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