Release notes for HUMAnN 3.0.0 and ChocoPhlAn 201901b

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: humann3 – The Huttenhower Lab.

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.

Thank you on behalf of the Nephele https://nephele.niaid.nih.gov/ team. We now have updated the the WGS pipeline we host on Nephele that is using biobakery workflows (0.13.2) and HUMAnN 3.0.

Hi, I am using the latest human(3) and metaphlan with the updated databases. My metagenomes are heavily dominated by fungal reads(70-80%). However, human does not classify most of the reads (90%). I also do not see any pathways associated to fungal reads. I have kept the command quite simple

humann --input $in --output $out --threads 64

Can you help me tweak the comment to maximise the eukaryote read classification?

Thanks for the great tool by the way.

Can you please copy this question to a new post?