[Bioperl-l] Bio::Index::Fastq indexing options

[Peter Cock]

On Mon, Jul 11, 2011 at 7:48 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Forgot to mention, for more info on this, see:
>
> http://www.bioperl.org/wiki/HOWTO:SQLite_for_BioPerl_indexing
>
> This is also filed in Redmine as a bug I believe.
>
> chris

We've got SQLite based indexing for Biopython's SeqIO module,
and I'd be keen to try and share the same format (table names,
column names etc). I view this as an extension to the existing
flat file and BDB backends for OBDA - what I did for Biopython
with SQLite was very much inspired by that design.

http://obda.open-bio.org/
http://lists.open-bio.org/pipermail/open-bio-l/2009-August/000561.html

If any BioPerl folk are at the CodeFest this week before BOSC,
this could be a good project:

http://www.open-bio.org/wiki/Codefest_2011

Peter