[Bioperl-l] Next-gen modules
cjfields at illinois.edu
Thu Jul 9 18:48:13 EDT 2009
Looks very promising. Do you know if it's capable of reporting back
indices, e.g. for building flat-file databases?
On Jul 9, 2009, at 3:42 PM, Matthew Vaughn wrote:
> 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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