On Thu, Oct 6, 2011 at 4:48 AM, Duddy, John <jdu...@illumina.com> wrote:
> One of the things we’re facing is the sheer size of a whole human genome at
> 30x coverage. An effective way to deal with that is by compressing the FASTQ
> files. That works for BWA and our ELAND, which can directly read a
> compressed FASTQ, but other tools crash when reading compressed FASTQ
> filesfiles. One way to address that would be to introduce a new type, for
> example “CompressedFastQ”, with a conversion to FASTQ defined. BWA could
> take both types as input. This would allow the best of both worlds –
> efficient storage and use by all existing tools.

We'd discussed this and a more general approach where any file
could be gzipped, but the code to do that doesn't exist yet:

Issue filed:

That seems a better long term solution than the pragmatic short term
solution of fastqsanger-gzip (or whatever it gets called). Note that it
sounded like Edward Kirton might already be using this - you should
be consistent.

The other strong idea from that thread was moving from FASTQ to
unaligned BAM, which is gzipped compressed, and has explicit
support for paired end reads, read groups, etc.


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