MetaPhlAn 4.2.5 release (minor code updates and database update)

Microbial community profiling MetaPhlAn
1

Announcement

We are pleased to share that MetaPhlAn 4.2.5 is now available, which incorporates minor code improvements and includes a new version of the MetaPhlAn database (vJan26_202605) containing >13k new SGBs.

For details on MetaPhlan 4, check announcing MetaPhlAn 4 or visit the MetaPhlAn 4 GitHub repository. For the full list of modifications and new features implemented in this new release check the MetaPhlAn 4.2.5 release notes.

What is new in MetaPhlAn 4.2.5

  • Improved usability of the sgb_to_gtdb.py utility script with automatic detection of the correct gtdb conversion file, possibility to provide a different conversion file and to provide a MetaPhlAn merged profile (flag --merged_profiles)

What has changed in vJan26_202605 in comparison to vJan25_202503

Expansion and improvement of the genomic database

  • ~561k new MAGs, spanning primates, food, and oral datasets among other environments

Expansion and improvement of the markers database

  • vJan26 includes 72,000 SGBs, 13,669 more SGBs than in vJan25. To see the full list of species in the database you can check out the file in mpa_vJan26_CHOCOPhlAnSGB_202605_species.txt.bz2

  • Improved gene family annotation with updated UniRef_202501 using Bakta v6.0 modified to support archaea

How to make use of the MetaPhlAn 4.2.5 updates

$ metaphlan --install --force_download

5 Likes
3

Thank you for the metaphlan update! I was able to install it with the 2026Chocophlan database.

Question about this statement: “Improved gene family annotation with updated UniRef_202501 using Bakta v6.0 modified to support archaea”. Is this in humann, or is there a way to get updated UniRef databases in humann? Right now all I see is the 2019 version. TY! :grinning_face: