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