Is there a DNA de-novo assembler parallelized for PBS/torque environment?

Question

[chefarov]

Hello all,

I was wondering if there exist a dna de-novo assembler which can exploit PBS/torque grid scheduler to perform the assembly process in parallel.

I am not interested in running N instances of an assembler changing a parameter (e.g k-mer length), I am interested in parallel execution of a single assembly process itself, which means an assembler implementing parallelization with PBS inherently.

Thanks

Answer 1

[Devon Ryan]

There won't be anything specifically for a given scheduler, since the scheduler you use doesn't really matter. What you're looking for is an assembler that can use MPI. I believe that ABySS and Ray support that and wouldn't be surprised if there are others (any tool that hopes to assemble a mammalian-sized genome is going to want to use a cluster).

[chefarov]

You are right, I probably misunderstood this. I suppose since MPI deals with distributing the work, any job scheduler would fit with the rest. Thanks