Hi all, I’m still running the “old” HUMAnN2 pipeline, but I suspect that reference databases are not up to date anymore.
I’m wondering if and where I could find the updated chocophlan, Uniref and metaphlan databases (i.e.: the same used for HUMANn3, if compatible) to be used in HUMANn2.
Thank you very much in advance
Marco
Unfortunately we don’t have bioBakery v3 databases formatted for use with bioBakery v2 software (and I worry that offering them would lead to confusion). I recommend either completing your analysis within the v2 framework OR upgrading both software and databases to v3.
Dear @franzosa, thank you very much for the prompt reply.
Following the link HUMANn2 gets its databases from (Index of /humann2_data/), there seem to be more recent databases than the ones automatically detected by the software via
“humann2_database --available” command.
Do you now if they are compatible with HUMANn2?
Thank you very much again.
Sorry for the slow reply. I think this is just a result of the HUMAnN 3 and 2 databases being hosted from the same location (which bears the older humann2 name in the path). The HUMAnN 3 databases are not backward compatible to HUMAnN 2.