I noticed metaphlan 4 was recently released. We use humann3 while providing a custom taxonomic table (bugs list). Is it possible to simply update the chocophlan database to the mpa_vJan21_CHOCOPhlAnSGB_NEW version, or do we need to also install metaphlan4 ? Any general guidelines or recommendations would be much appreciated.
This is something we’re working on. The file you’re seeing (
mpa_vJan21_CHOCOPhlAnSGB_NEW) corresponds to marker genes for SGB pangenomes for taxonomic profiling with MetaPhlAn. These are not the full pangenomes (as required by HUMAnN). Efficient mapping to the full SGB pangenome collection is something we’re targeting for HUMAnN 4.0. We plan to release a “bridge” version of HUMAnN (tentatively called v3.5) in the shorter term that will allow users to combine SGB-based taxonomic profiles with the previous generation (v3) pangenomes. I’ll make a pinned note about that in this forum when it’s ready.