Bowtie2 parallelization on cluster
1
0
Entering edit mode
7.4 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 • 2.3k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
7.4 years ago
erictleung ▴ 120

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1438 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6