[Bioperl-l] Next-gen modules
e.stupka at ucl.ac.uk
Wed Jun 17 07:29:08 EDT 2009
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
Office (UCL): +44 207 679 6493
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