Bowtie2 parallelization on cluster
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.
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erictleung
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rbronste
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rbronste
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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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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.