[Bioperl-l] Next-gen modules

Mark A. Jensen maj at fortinbras.us
Wed Jun 17 08:02:11 EDT 2009

I say a definite +1; in fact, this sounds like it should be a Hot Topic 
(see http://www.bioperl.org/wiki/Category:Hot_Topics for some others
you might have missed in your hiatus...). I will create a page that 
can be a central point for wish lists, discussion, etc.

There has been much discussion of late about FASTQ 

cheers from a newbie, 

----- Original Message ----- 
From: "Elia Stupka" <e.stupka at ucl.ac.uk>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, June 17, 2009 7:29 AM
Subject: [Bioperl-l] Next-gen modules

> 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
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> University College London
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