[Bioperl-l] Next-gen modules

Lincoln Stein lincoln.stein at gmail.com
Sat Jun 20 17:01:43 EDT 2009

Hi All,

Apropos of this, I am about to release to CPAN a BioPerl interface to SAM
and BAM files. The documentation is still in progress, but you can get CVS
access here:

% cvs -d :pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod co


On Wed, Jun 17, 2009 at 7:29 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:

> Dear all,
> after several years of absence I am slowly coming back to Bioperl, and hope
> to contribute again to its development.
> One area that I was thinking of starting from, since we are actively
> involved with it, is to improve BIoperl's support fo next-gen sequencing
> data, tools, etc. Since I am sure I have missed out on a lot of recent
> developments, do let me know if/what is useful.
> One example that comes to mind is that the conversion of various formats
> to/from FASTQ does not seem to be supported. Some code can be found within
> Li Heng's script: http://maq.sourceforge.net/fq_all2std.pl but it would be
> good if it could make its way into SeqIO? And similarly, potentially, for
> other next-gen sequence formats?
> Similarly, there seems to be little in bioperl-run to support tools that
> have been developed in this area, such as Maq, BowTie, TopHat, etc?
> Do let me know if there is a past thread on this, or other people actively
> developing, etc. so that I can find out what priorities are.
> thanks and best regards to all (old friends and new),
> Elia
> ---
> Senior Lecturer, Bioinformatics
> UCL Cancer Institute
> Paul O' Gorman Building
> University College London
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> London
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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

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