[Bioperl-l] Next-gen modules

Chris Fields 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?

chris

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.
>
> Matt
>
> --
> 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
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> google-talk: matt.vaughn at gmail.com
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