[Bioperl-l] SFF format support

Peter biopython at maubp.freeserve.co.uk
Wed Nov 3 14:28:56 UTC 2010

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Hi all,
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
> Does anyone already took this?
> Best regards,
> M;


This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.


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