Announcing HUMAnN 3.5

HUMAnN 3.5 Release Notes

HUMAnN 3.5 provides compatibility between the newly released MetaPhlAn 4 taxonomic profiling system and the existing bioBakery 3 infrastructure.

What has changed in HUMAnN 3.5:

  • HUMAnN 3.5 maps MetaPhlAn 4’s species genome bin (SGB)-based taxonomic profiles to the existing bioBakery 3 pangenomes (as recently updated with HUMAnN 3.1).

  • Due to their independent construction, SGBs can map to bioBakery 3 pangenomes in a variety of ways (one-to-one, one-to-many, one-to-none, or many-to-one). The details of these mappings are included in the HUMAnN 3.5 log files.

What has NOT changed in HUMAnN 3.5:

  • HUMAnN 3.5 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 3.5 remains backward compatible with MetaPhlAn 3 taxonomic profiles (including MetaPhlAn 4 run with the v3.1 marker gene database).

How to perform a fresh install of MetaPhlAn 4 and HUMAnN 3.5:

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

  • Upgrading MetaPhlAn:

    • $ conda install -c bioconda metaphlan=4.0.0
  • Upgrading HUMAnN software:

    • $ pip install humann --upgrade

    • 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 3.5. You can point your HUMAnN 3.5 installation to the locations of these existing files using the humann_config script.

What’s next

  • HUMAnN 4 is in development and will allow native mapping to the SGB pangenomes profiled by MetaPhlAn 4.
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