I carried out a HUMAnN 3 analysis which, by default, relies on MetaCyc database. My collaborator asked me if I could do a KEGG pathway analysis instead. I think I could based on the documentation I read, but what are the advantages and disadvantages of each? I wonder if changing my pipeline is worthwhile.
The MetaCyc authors offer a comparison with KEGG in their 2020 update paper that might be of use to you:
Excellent recommendation. Thank you.