# Optimal thread count for KneadData, Bowtie2, MetaPhlAn, and HUMAnN on multi-core systems

**URL:** <https://forum.biobakery.org/t/optimal-thread-count-for-kneaddata-bowtie2-metaphlan-and-humann-on-multi-core-systems/8467>\
**Category:** HUMAnN\
**Created:** [September 3, 2025, 1:56am UTC](https://forum.biobakery.org/t/optimal-thread-count-for-kneaddata-bowtie2-metaphlan-and-humann-on-multi-core-systems/8467 "2025-09-03T01:56:19Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gy.park](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/gy.park/32/3353_2.png) [@gy.park](https://forum.biobakery.org/u/gy.park)\
**Post date:** [September 3, 2025, 1:56am UTC](https://forum.biobakery.org/t/optimal-thread-count-for-kneaddata-bowtie2-metaphlan-and-humann-on-multi-core-systems/8467/1 "2025-09-03T01:56:19Z")

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Hi BioBakery team and fellow users,

I’m running a metagenomic pipeline using KneadData, Bowtie2, MetaPhlAn, and HUMAnN on a multi-core system (dual-socket, 24 physical cores per socket).

Specifically, I’m curious:

- For each tool (KneadData, Bowtie2, MetaPhlAn, HUMAnN), which thread count (e.g., 8, 16, 24, 32) generally gives the best balance of runtime efficiency and resource utilization?
- At which thread point does performance plateau or degrade (i.e., adding more threads yields little to no speedup)?
- Have others observed “sweet spots” for each tool on similar high-core-count servers (e.g. 48, 64, 96 threads)?

I’d appreciate sharing any benchmark data, personal experience, or guidance from the devs. Thank you for your help!

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [November 4, 2025, 9:09pm UTC](https://forum.biobakery.org/t/optimal-thread-count-for-kneaddata-bowtie2-metaphlan-and-humann-on-multi-core-systems/8467/2 "2025-11-04T21:09:53Z")

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I tend to throw 8 threads at MetaPhlAn + HUMAnN. That definitely gives a nice performance boost over a single thread but I think it starts to degrade after that. It’s been a long time since I actually benchmarked it though!