[Bioperl-l] Bio::Index::Fastq - Interface for indexing (multiple) fastq files failure

Peter biopython at maubp.freeserve.co.uk
Wed Apr 7 11:45:54 EDT 2010


On Wed, Apr 7, 2010 at 4:25 PM, Cook, Malcolm <MEC at stowers.org> wrote:
> c.f. http://github.com/acr/screed

That's the python thing I referred to earlier, which turned out to be much
slower than SQLite (comparing storing the FASTQ data in an indexed
form, not just storing the file offsets):

http://lists.idyll.org/pipermail/biology-in-python/2010-March/000511.html
http://ivory.idyll.org/blog/mar-10/storing-and-retrieving-sequences.html

Peter


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