[Biopython-dev] sff reader

Senthil Palanisami spenthil at gmail.com
Sat May 23 01:48:24 UTC 2009

Sorry, I only recently joined this list - should have gone through the
archives first.

I have done some minimal SFF tweaking, but only by first converting them to
CA format.

No paired end reads yet, but I do know my PI wants me to start looking at
some in the next month or two.

Senthil Palanisami

On Fri, May 22, 2009 at 5:10 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On 5/23/09, Senthil Palanisami <spenthil at gmail.com> wrote:
> > I have been working with SFF files for the past month, and can say it's
> >  definitely frustrating working with custom binary formats.
> At least in this case it is publicly documented. Have you needed to
> write out (or edit) an SFF file yet? Have you used any paired end
> reads in SFF format?
> >  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
> That is what this code is based on - Jose Blanca is one of the authors
> of  sff_extract.
> >  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
> I think you must have missed this thread last month ;)
> http://lists.open-bio.org/pipermail/biopython/2009-April/005084.html
> Peter

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