How to use a custom KEGG database?

[BenWu1224]

Hello, I am a beginner in using Picrust2. I previously attempted to use the KEGG database but found out that it is now a paid service, so I abandoned the idea. However, I have recently obtained a legally obtained KEGG database through school funding, but it is apparent that the overall format is significantly different from the default MetaCyc database in the pathway_mapfile I have checked. The KEGG database I obtained mainly consists of ''ko.list'', which is a table linking pathways to KOs, and ''xxxx.conf'', which contains details within each pathway. I would like to ask if any experienced users have successfully converted this type of database into a usable format. Thank you all for your responses.

Note: .conf contains lots of 'circ (483,230) 4 /dbget-bin/www_bget?C00668 C00668 (alpha-D-Glucose 6-phosphate)', which is quite different from metacyc database. And ko.list contains lots of ''path:ko00010 ko:K00138'' .

[Gavin Douglas]

Hi there,

You can see the pathway mapfile for the last openly available version of KEGG here: https://github.com/picrust/picrust2/blob/master/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv

So if you formatted your files in this format as well it should be straight-forward to plug into PICRUSt2.

Cheers,

Gavin