[AdrianP]

Quick Question, does Ray support hybrid assembly? 454 and illumina? Can ray do a reference assembly? Is there GUI?

I almost got to using RAY but had huge problems with openmpi.

Adrian

[seb567]

Quick Question, does Ray support hybrid assembly?

Yes.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Sébastien Boisvert, François Laviolette, and Jacques Corbeil.
Journal of Computational Biology (Mary Ann Liebert, Inc. publishers).
November 2010, 17(11): 1519-1533.
doi:10.1089/cmb.2009.0238

See others here too: http://denovoassembler.sourceforge.n...lications.html

454 and illumina?

Yes. See paper above.

Can ray do a reference assembly?

No. Ray only does de novo stuff.

Is there GUI?

Not in the vanilla, but I know that Applied Maths Inc. is working on one.

See http://www.applied-maths.com/opensource/opensource.htm

I almost got to using RAY but had huge problems with openmpi.

Adrian

Open-MPI is very easy to install. If you have a decent GNU/Linux distribution, then you can install it right away as a package.

Otherwise:

wget http://www.open-mpi.org/software/omp...-1.4.3.tar.bz2
tar xjf openmpi-1.4.3.tar.bz2
cd openmpi-1.4.3
./configure --prefix=$(pwd)/build
make
make install

You now have Open-MPI in $(pwd)/build

In particular, $(pwd)/build/bin/mpic++ and $(pwd)/build/bin/mpirun.

Now add $(pwd)/build/bin to your path.

For example in your .bashrc:

export PATH=/home/boiseb01/software/openmpi-1.4.1/build/bin:$PATH


Anyway, you should use a decent GNU/Linux distribution -- it makes things easier.