[Bioperl-l] Next-gen modules
vaughn at cshl.edu
Thu Jul 9 16:42:53 EDT 2009
A lot of what is being discussed is handled very elegantly by Assaf
Gordon's FASTX toolkit <http://hannonlab.cshl.edu/fastx_toolkit/>. I
spent a lot of time trying to roll my own solutions for basic Illumina
processing and I've found his utilities to work much more reliably and
very fast (almost real-time) than anything I could design in Perl.
They are also the basis for Illumina handling in Galaxy, which is a
second vote of confidence.
They've got clean CLI interfaces and should be very easy to wrap in
Bio::SeqUtils or Bio::Run packages.
Matthew W. Vaughn, Ph.D.
Research Assistant Professor
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
tel: (516) 367-8808
cell: (516) 353-7055
google-talk: matt.vaughn at gmail.com
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