On Thu, Sep 1, 2011 at 11:02 PM, Edward Kirton <eskir...@lbl.gov> wrote:
> Read QC intermediate files account for most of the storage used on our
> galaxy site. And it's a real problem that I must solve soon.
> My first attempt at taming the beast was to try to create a single read QC
> tool that did such things as convert qual encoding, qual-end trimming, etc.
> (very basic functions).  Such a tool could simply be a wrapper around your
> favorite existing tools, but doesn't keep the intermediate files.  The added
> benefit is that it runs faster because it only has to queue onto the cluster
> once.
> Sure, one might argue that it's nice to have all the intermediate files just
> in case you wish to review them, but in practice, I have found this happens
> relatively infrequently and is too expensive.  If you're a small lab maybe
> that's fine, but if you generate a lot of sequence, a more production-line
> approach is reasonable.

Sounds very sensible if you have some frequently repeated multistep

> I've been toying with the idea of replacing all the fastq datatypes with a
> single fastq datatype that is sanger-encoded and gzipped.  I think gzipped
> reads files are about 1/4 of the unpacked version.  Of course, many tools
> will require a wrapper if they don't accept gzipped input, but that's
> trivial (and many already support compressed reads).
> However the import tool automatically uncompressed uploaded files so I'd
> need to do some hacking there to prevent this.

Hmm. Probably there are some tasks where a gzip'd FASTQ isn't
ideal, but for the fairly typical case of intreating over the records
it should be fine.

> Heck, what we really need is a nice compact binary format for reads, perhaps
> which doesn't even store ids (although pairing would need to be recorded).
> Thoughts?

What, like a BAM file of unaligned reads? Uses gzip compression, and
tracks the pairing information explicitly :) Some tools will already take
this as an input format, but not all.


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