[Open-bio-l] More FASTQ examples for cross project testing

[Peter]

On Tue, Aug 25, 2009 at 12:24 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> I've been chatting with Peter Rice (EMBOSS) and Chris Fields (BioPerl)
> off list about this plan. I'm going to co-ordinate putting together a
> set of valid FASTQ files for shared testing (to supplement the
> existing set of invalid FASTQ files already done and being used in
> Biopython and BioPerl's unit tests - and hopefully with EMBOSS soon).
>
> What I have in mind is:
>
> XXX_original_YYY.fastq - sample input
> XXX_as_sanger.fastq - reference output
> XXX_as_solexa.fastq - reference output
> XXX_as_illumina.fastq - reference output
>
> where XXX is some name (e.g. wrapped1, wrapped2, shortreads,
> longreads, sanger_full_range, solexa_full_range ...) and YYY is the
> FASTQ variant (sanger, solexa or illumina) for the "input" file.

I didn't want to clog up the mailing list with attachments, but just
for the record, I've sent my first attempt at this to Peter (EMBOSS)
and Chris (BioPerl) for comment (and checking).

My earlier set of error_*.fastq files are in Biopython CVS/github and
have since been copied to BioPerl SVN as well.

Peter