Multi threading bowtie index

Question

[ChillarAnand]

When building index of an organism using bowtie2-build, system is using only 1 core and less than 10% of memory(out of 64 GB) which is poor resource usage.

Is there a way to make indexing faster using bowtie2-build or how to make bowtie2 to consume more cores and memory so that indexing becomes faster?

[Brian Bushnell]

As Devon said, there's nothing you can do about it (without rewriting the code). If you're working with a single organism with a fixed reference, it normally does not matter too much as you only need to index it once. But if you are dealing with a lot of organisms, or a lot of assemblies of the same organism, I encourage you to check out BBMap, which is multithreaded in the indexing phase and thus finishes very quickly; typically around 3 minutes for a human-size genome.

[ChillarAnand]

BBmap looks good. Thank you!

Answer 1

[Devon Ryan]

It's a single threaded application, there's nothing that you can do.

Answer 2

[Pratik]

New update.. Now you can use bowtie2-buildwith multi-thread option.. the flag is --threads.

[ATpoint]

Thanks for the update, but it was added in version 2.2.7 dating back to 2016 ;-) so it's not exactly "new".

See https://bowtie-bio.sourceforge.net/bowtie2/news.shtml