Question about KO hierarchy output in PICRUSt2 pipeline

[ShahariarArif]

Hello PICRUSt2 team,

I am using PICRUSt2 v2.6.2 to generate KO abundances from 16S data. I have a question regarding the output tables:

Is there a recommended way to produce a TSV that includes full KEGG pathway hierarchy levels (level 1, 2, 3) for each KO directly from the pipeline?

The current output (pred_metagenome_unstrat.tsv) lists KO abundances but does not include hierarchy annotations.

I am also attaching screenshots of the output for clarity.

Any guidance on how to obtain a KO abundance table with full pathway hierarchy would be greatly appreciated.

Thank you!

[R-Wright-1]

Hi there,

Unfortunately this isn't something that we can do. The KO information that we provide comes from EggNOG and it is possible to add descriptions (using the add_descriptions.py script) that come from the HUMAnN files, but as the hierarchical KEGG information is not publicly accessible without paying for licensing, we can't provide these files to PICRUSt2 users.

If you have a license to the KEGG database then you would simply need to make a file with this hierarchical information in the same format as the existing KO file here, and then you could use the add_descriptions.py script with the --custom_map_table option.

Best wishes,
Robyn

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