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

Evan Staton statonse at uga.edu
Mon Jul 11 18:33:19 UTC 2011

Hi bioperl-l,

I have been experimenting with Bio::Index::Fastq, and I realize from
previous conversations<http://lists.open-bio.org/pipermail/bioperl-l/2011-February/034530.html>
the list that this module will not work efficiently with the scale of Fastq
files being produced by modern sequencing instruments. Based on that
conversation, it appears that the module uses DB_File currently and it was
mentioned that AnyDBM_File could be used to allow the use of SQLite. Has any
progress been made towards this goal? I am aware there are other indexing
solutions, and I would offer to help out but it appears this transition has
already been worked out in detail on the
However, I don't see the changes reflected in github for this module. I was
curious if the performance improvements did not justify making changes for
this module or if there were other explanations.

Sorry if I missed relevant conversations on the topic, but I'd like to help
with this if I can.



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