The bioBakery help forum

Kegg on Humann2


I was wondering if there was a way to get the keggpathways from Humann2 without installing Humann legacy. I am trying to confirm data I obtained containing metacyc pathways.

Is this possible without using the humann_legacy program and if that isnt the case, does anyone know where I can find a KEGG database folder to implement?


I am also interested in mapping the MetaCyc output to KEGG pathways. Most of the online instructions for this process seem outdated. Any help would be appreciated!


HUMAnN 2.0 does not automatically generate KEGG pathway output. The manual provides instructions on how to generate KEGG pathway output using Legacy HUMAnN 1.0 functionality, but I agree that those results would be outdated at this point.

If you are able to download and reformat modern KEGG pathways on your own, you can use the regroup script to convert UniRef abundance to KO abundance and then provide KO abundance + KEGG pathway definitions to HUMAnN 2.0 to compute pathway abundance.

We’re looking into including KEGG pathways + modules as a MetaCyc alternative in the next iteration of HUMAnN.