[Bioperl-l] fastq splitter

Peter Cock p.j.a.cock at googlemail.com
Wed Feb 29 05:32:20 EST 2012


On Wed, Feb 29, 2012 at 2:42 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Frankly, there never seemed to be a real fixed standard in the way that FASTQ
> headers were written (and just when it seems there is some consensus, Illumina
> pulls the rug out from under you), hence the reason I leave it alone.  We could
> add some ID munging in there if needed, would just need a qr// with a standard
> fallback.
>
> chris

Indeed - just like FASTA, it seems every company/tool/database has its own
conventions about the FASTQ ID line and how to stuff as much meta-data
into it as possible. This is a major reason why I hope unaligned reads in
SAM/BAM takes off - places like the Sanger and Broad use this in their
pipelines.

http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html

Peter



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