Dear HUMAnN and bioBakery teams,
I am writing to ask for an update on the status of the next major HUMAnN 4 release. We have now been on the alpha version of v4 for over 2 years, and while I understand the demands of managing a large lab with many projects, it has started to become quite an issue that the data versions available for MetaPhlAn vs HUMAnN (as discussed in detail on this forum already) have diverged so much. I frequently have to explain to collaborators why the species present as contributors to functions seem to be so different from those that we’ve identified as present in the community. It’s also not clear to us whether the current best practice for controlling this issue is to continue using HUMAnN v3.9, which can handle up to vJun23 markers, but remains at v2019b pangenomes; or to use the current v4 alpha, which downgrades markers to vOct22, but also uses vOct22 pangenomes (I assume, I have not been able to confirm this, the pangenomes are listed only as ‘v4’).
Could you please provide insight into the current status of v4 development? Even a rough, non-binding estimate of when the full v4 might be released would be helpful for deciding what to use in the interim.
Best,
Adam Cantor
Clemente Lab
Icahn School of Medicine at Mount Sinai