[Biojava-l] FASTQ in BioJava, BioRuby (and Biopython, BioPerl & EMBOSS)

[Andreas Prlic]

Hi Peter,

I would be happy to have support for the FASTQ file format in BioJava.
We had an increased number of requests for parsing the output of
sequencing machines in the last weeks, but nobody has stepped up to be
module-lead for this as of yet. I am currently not working with
sequencers myself, so I can't  really provide support for this. I am
happy to help anybody who wants to be module lead for this to get this
going.

Andreas


On Wed, Jul 29, 2009 at 3:10 AM, Peter Cock<p.j.a.cock at googlemail.com> wrote:
> Dear Andreas (& Richard) and Goto-san,
>
> Are BioJava or BioRuby interested in supporting the FASTQ file format
> used in next generation sequencing for storing sequencing reads with
> associated quality scores?
>
> I have been working on FASTQ support in Biopython, and coordinating
> with Peter Rice at EMBOSS and Chris Fields at BioPerl to ensure we
> are consistent on our interpretation of these files, interconversion, and
> naming. We'd like to get BioJava and BioRuby involved too.
>
> Please could you (or whomever at BioJava/BioRuby would be doing
> FASTQ code) please sign up to the cross-project OBF mailing list?
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>
> Thank you,
>
> Peter
> --
> Dr Peter Cock, Biopython project
>