HUMAnN 3.8 Release Notes

Microbial community profiling HUMAnN
1

Summary:

  • HUMAnN 3.8 makes small improvements to compatibility with the current (vOct22) and future MetaPhlAn 4 marker databases. It also implements a small improvement related to quantifying multipart metabolic reactions.

What has changed in HUMAnN 3.8:

  • HUMAnN 3.8 incorporates an improved mapping between bioBakery v3.1 pangenomes and the MetaPhlAn vOct22 SGB marker database. This mapping now better captures highly similar SGBs that were merged into “SGB groups” during the marker creation process. Such SGBs are a small minority of the overall database.

  • We have also made a small change to the pathway quantification algorithm to better handle multipart metabolic reactions. These reactions are variably coded in genomes and pathways as either a single reaction (e.g. A) or a pair of required reactions (B & C). HUMAnN will now optimize over A | (B & C) in pathways where these multipart reactions are present. This adds robustness to cases where (for example) a pathway is annotated as requiring A while a pangenome is annotated as having B and C but not A.

What has NOT changed in HUMAnN 3.8:

  • HUMAnN 3.8 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 3.8 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 3.8:

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 3.8. You can point your HUMAnN 3.8 installation to the locations of these existing files using the humann_config script.

What’s next:

  • HUMAnN 4 remains on-track for its public v4.0.0.alpha.1 release at the end of this summer.