[Bioperl-l] Next-gen modules

Matthew Vaughn vaughn at cshl.edu
Thu Jul 9 20:42:53 UTC 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
Williams #5
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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