Announcing HUMAnN 3.9


  • HUMAnN 3.9 enables tiered search using MetaPhlAn 4.1’s recently updated marker database (June 2023 version) and the bioBakery 3.1 pangenome catalog.

  • HUMAnN 3.9 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 3.9 remains backward compatible with MetaPhlAn 3.1 taxonomic profiles (including MetaPhlAn 4.1 run with the v3.1 marker gene database).

How to perform a fresh install of MetaPhlAn 4.1 and HUMAnN 3.9:

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=4.1.0

  • 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 3.9. You can point your HUMAnN 3.9 installation to the locations of these existing files using the humann_config script.

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