Request for Higher Taxonomic Level Analysis in HUMAnN

Dear HUMAnN Development Team,

I am currently utilizing the HUMAnN software for metagenomic analysis, specifically interested in taxonomic characterization at various levels of resolution. The output I am receiving is at the species level by default, and I have successfully used the humann_genefamilies_genus_level command to obtain results at the genus level. However, my research requires analysis at higher taxonomic levels beyond genus.

Could you please advise if there is a way to modify the output to include higher taxonomic levels (e.g., family, order, class, phylum)? If such functionality exists, I would greatly appreciate guidance on how to implement this.

Additionally, if there are any workarounds or recommended practices for achieving these results using the current version of HUMAnN, your insights would be invaluable.

Thank you for your time and support. I look forward to your response.

Best regards,

This is possible using the infer_taxonony script at the UniRef90/50 level and specifying a rank above species (I believe “genus” is the default). You can then provide the higher-ranked UniRef90/50 inputs back to HUMAnN to quantify reactions and pathways above the species level.