Using humann2_infer_taxonomy and/or uniref90-tol-lca.dat to assign taxonomy to UniRef90 hits

Microbial community profiling HUMAnN
1

Hi HUMAnN2 team,
I’m working on assigning taxonomy to UniRef90 hits and would like to integrate into the HUMAnN2 environment for taxonomic assignments of hits. I have output from a diamond blastx vs UniRef90 run so UniRef90 IDs as well as a pipe character followed by a string, e.g., UniRef90_R5XQM2 and UniRef90_R5XQM2|1416. I tried joining the UniRef90_R5XQM2 on your uniref90-tol-lca.dat file but this offers pretty limited taxonomic information where I would expect something deeper. Is there a way to use your humann2_infer_taxonomy on diamond blastx vs UniRef90 runs?

The reason I’m not using the HUMAnN2 pipeline is that I’m working in an environment with a ton of novelty, so had to build my own gene catalogue and am checking annotations across several databases (UniRef, PFAM, KEGG etc.). I understand this is outside the scope of using the HUMAnN2 pipeline but was hoping you can offer some guidance nonetheless. Thank you!

2

Can you expand on the deeper taxonomic info you’re looking for? The tol-lca file gives the LCA for the UniRef family as defined in UniRef (i.e. the LCA of all species contributing a protein to the family).

3

Ah, ok, I misunderstood the file and that makes sense. I tried going through the huamnn2_infer_taxonomy script and it seemed like something more complicated was going on. So, a join on diamond blastx vs UniRef90 output by UniRef90 ID with the LCA file is sufficient for LCA taxonomic assignment?

4

Yes, that should allow you to add the NCBI TaxID for the LCA to your blast output table.