[Open-bio-l] FASTQ in BioRuby?

[Naohisa GOTO]

Hello Peter,

sorry for responding too late. I've subscribed to open-bio-l,
but I could not actively join to the discussions, because of
lack of my knowledge about FASTQ.

There is a small primitive code attempt to support FASTQ format
in BioRuby, which is not yet merged in the main repository.
http://github.com/ngoto/bioruby/tree/master

Recently, Anthony Underwood contributed chromatgram classes
to support SCF/ABI formats, which will be merged soon,
after bug-fix maintenance release of 1.3.1.
http://github.com/aunderwo/bioruby/tree/master

I'm now planning to rewrite my FASTQ code to be consistent
with the chromatgram classes, and with the open-bio standards.

Thank you,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 27 Aug 2009 11:46:17 +0100
Peter <biopython at maubp.freeserve.co.uk> wrote:

> Hello BioRuby team,
> 
> I am one of the Biopython developers, and together with Peter Rice
> (EMBOSS) and Chris Fields (BioPerl) we have been coordinating
> how these Open Bioinformatics Foundation (OBF) projects will
> interpret the FASTQ file format used in next generation sequencing.
> 
> This includes standardising our naming conventions for the original
> Sanger FASTQ variant, and the later Solexa/early Illumina, and
> recent Illumina 1.3+ variants. We have also put together a set of
> test files, including reference conversions between the different
> FASTQ variants.
> 
> We would be delighted to get BioRuby involved. I tried to contact
> Naohisa Goto about this directly last month, but perhaps my email
> did not arrive. If BioRuby is working on (or planning to work on)
> FASTQ support, please could the developers concerned sign up
> to the OBF joint mailing list where we have been discussing this:
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thank you,
> 
> Peter
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