Bowtie2 parallelization on cluster

Question

[rbronste]

Hi,

Looking for optimal settings to run Bowtie2 on high performance cluster, in terms of memory allocation and assignment of parallel nodes etc. Thanks.

Rob.

[GenoMax]

You do not want to spread the threads across physical nodes. You will get the best performance by using (and keeping) the most cores you can assign on a physical node.You could brute-force parallelize overall workload further by splitting query fasta files into multiple pieces.

Answer 1

[erictleung]

You can use the -p option to specify the number of parallel search threads (see http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#performance-tuning for more performance information). The manual in general has lots of good information on how to use Bowtie2. Good luck.