On Tue, Nov 8, 2011 at 11:45 PM, Duddy, John <jdu...@illumina.com> wrote:
> It's not public yet, and it involves a little conundrum - we want
> it so we can support large amounts of data efficiently on a variety
> of aligners, including our ELAND from CASAVA. However, ELAND
> does not support unaligned BAM inputs yet, and apparently it
> would be a lot of work to make it so (and another team's area
> of responsibility as well).

OK, so using (unaligned) BAM isn't about to happen.

> So in the near term, BGZF would not meet our needs.

I don't follow you there, BAM != BGZF.

We can use BGZF to compress FASTQ, FASTA, GenBank,
basically anything. You get compression approaching that
of plain GZIP (depending on the characteristics of the data)
plus efficient random access.

> However, work is quite far along on a GZIP-based one
> that works with ELAND and BWA, since they both read
> GZIP FASTQ files, and works/will work with a converter
> to fastq_sanger for other tools.
> I can put you in touch with the engineer doing the work if
> you are interested.

That might be a good idea, or ask them to post here?

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