[Bioperl-l] Next-gen modules

Elia Stupka e.stupka at ucl.ac.uk
Wed Jun 17 07:29:08 EDT 2009

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),


Senior Lecturer, Bioinformatics
UCL Cancer Institute
Paul O' Gorman Building
University College London
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