[Bioperl-l] Maq assembly wrapper ready for beta testing

Mark A. Jensen maj at fortinbras.us
Wed Nov 11 18:48:33 EST 2009

Hi All-

New modules are available in the core and in bioperl-run for
working with Heng Li's short read assembler "maq"
(http://maq.sourceforge.net/maq-man.shtml). Bio::Tools::Run::Maq
allows a quick assembly call with a canned a maq pipeline, and also
allows individual maq commands to be called separately. 
It uses Bio::Assembly::IO::maq  (a read-only module) to deliver
a Bio::Assembly::Scaffold from maq output. 

If you're interested, see
and update your core and bioperl-run. The code inherits from Florent's
excellent new Bio::Tools::Run::AssemblerBase -- kudos to him!!

tests are in bioperl-run/trunk/t/Maq.t, see them for myriad examples
send me the bugs

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