Question: Is there a DNA de-novo assembler parallelized for PBS/torque environment?
gravatar for chefarov
5.9 years ago by
chefarov130 wrote:

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.




ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 5.9 years ago by chefarov130
gravatar for Devon Ryan
5.9 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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).

ADD COMMENTlink written 5.9 years ago by Devon Ryan97k

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

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by chefarov130
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