Hi All - HUMAnN 3.0.0 has been out in the wild for a little while now, but I was slow in getting these release notes together. Please reply with any questions. Thanks! -Eric
Introduction
- HUMAnN 3.0.0 is a major update to HUMAnN (ending the HUMAnN 3.0.0.alpha lineage). Users will need to update their HUMAnN software and all database files for this release. Installation instructions can be found here: http://huttenhower.sph.harvard.edu/humann.
Database updates
-
The ChocoPhlAn database has been updated with ~600 additional species pangenomes that were missing from the previous release. This and other updated databases are tagged “201901b” to differentiate them from the previous (“201901”) release.
-
The UniRef protein databases have been re-indexed for the latest DIAMOND 0.x format (HUMAnN has not transitioned to DIAMOND 2.0).
-
MetaCyc pathway definitions and related information have been updated to release 24.0.
-
The utility mapping database has been updated with expanded UniRef-to-EC maps, updated UniRef taxonomy maps, and a much-requested UniRef90-to-UniRef50 map.
Performance updates
-
Changed a behavior that caused pangenomes of close relatives of MetaPhlAn-detected species (including many redundant CAG species) to be automatically added to the sample-specific pangenome index.
-
Improved memory efficiency during post-processing of mapping results.
Tool updates
-
The functionality of the
humann_infer_taxonomy
tool (which assigns putative taxonomy to unclassified UniRef abundance) has been restored and improved using new error-corrected UniRef LCA definitions. -
The
humann_barplot
tool has been redesigned to label more community species and to facilitate cross-plot consistency. -
Several HUMAnN 2.0-era experimental tools have been deprecated.
Quality-of-life changes
-
The HUMAnN command-line interface has been reorganized to group together related arguments (e.g. all arguments related to translated search).
-
Miscellaneous small bug fixes.