Question: Is there a DNA de-novo assembler parallelized for PBS/torque environment?
0
gravatar for chefarov
5.9 years ago by
chefarov130
Greece
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.

 

Thanks

 

ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 5.9 years ago by chefarov130
2
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
1

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1235 users visited in the last hour