Announcing HUMAnN 3.7

Microbial community profiling HUMAnN
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Summary:

  • HUMAnN 3.7 enables tiered search using MetaPhlAn 4’s recently updated marker database (October 2022 version) and the bioBakery 3.1 pangenome catalog.

What has changed in HUMAnN 3.7:

  • HUMAnN 3.7 maps MetaPhlAn 4’s species genome bin (SGB)-based taxonomic profiles (October 2022 version) to the existing bioBakery 3.1 pangenomes.

  • The procedure for associating SGBs with bioBakery 3.1 pangenomes has been simplified to facilitate continued interoperability between HUMAnN 3 and future versions of MetaPhlAn 4. Briefly, if an SGB X is detected by MetaPhlAn 4, and this SGB includes a reference genome Y, HUMAnN will map reads against the v3.1 pangenome that contains genome Y (if available).

  • As before, this means that a given SGB can cover multiple v3.1 pangenomes, or multiple v3.1 pangenomes can be covered by a single SGB. The details of these mappings are included in the HUMAnN 3.7 log files.

What has NOT changed in HUMAnN 3.7:

  • HUMAnN 3.7 is a software update only. If you are already using the most recent HUMAnN release (v3.1), there is no need to update your HUMAnN databases to use this version of the software.

  • HUMAnN 3.7 remains backward compatible with MetaPhlAn 3.1 taxonomic profiles (including MetaPhlAn 4 run with the v3.1 marker gene database).

How to perform a fresh install of MetaPhlAn 4 and HUMAnN 3.7:

How to upgrade from earlier versions of MetaPhlAn and HUMAnN 3:

  • $ pip install humann --upgrade (will upgrade the existing HUMAnN software)

  • $ conda install -c bioconda metaphlan=4.0.6

  • You DO NOT need to re-download the latest (v3.1) pangenome database, the DIAMOND-formatted UniRef90/50 databases, or the accessory mapping files to use HUMAnN 3.7. You can point your HUMAnN 3.7 installation to the locations of these existing files using the humann_config script.

What’s next:

  • HUMAnN 4 is approaching a v4.0.0.alpha.1 release and will allow native mapping to the SGB pangenomes profiled by MetaPhlAn 4.
2 Likes
3

Thanks for the update! Can you tag a new release on GitHub? Does 3.7 have a fix for the single-threaded bowtie-build step?

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Thanks for catching this: the v3.7 tag should now show up in the repo.

Multithreaded indexing has been implemented in the upcoming HUMAnN 4.0, but is not a part of this point release. This and future HUMAnN 3 point releases are/will be focused on correcting critical software/database issues and maintaining compatibility with MetaPhlAn 4.