I'm currently playing around with putting together an assembly pipeline that will merge the contigs generated from assembly of same input data with different parameters.
My current assembler of choice for working with 454 data is Newbler.
It can only handle input reads as long as 2000 bases. Shredding the initial contigs is an option but I have been told that Newbler has difficulty putting these contigs back together again.
Minimus2, part of the AMOS package, is made just for that. The latest addition to the minimus tools is minimus2-blat, which is possibly the fastest of the three minimus2 tools.
Here's how to install it:
mkdir AMOS
cd AMOS
cvs -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos login
cvs -z3 -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS
./bootstrap
./configure
make
make install
Tuesday, May 31, 2011
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