[Bioperl-l] Next-gen modules
Elia Stupka
e.stupka at ucl.ac.uk
Wed Jun 17 11:29:08 UTC 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),
Elia
---
Senior Lecturer, Bioinformatics
UCL Cancer Institute
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University College London
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