Bowtie2 parallelization on cluster
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6.6 years ago
rbronste ▴ 420

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.

Bowtie2 alignment • 2.0k views
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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.

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6.6 years ago
erictleung ▴ 110

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.

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