In order to reconstruct the metabolic activities of microbiome communities, the HMP Metabolic Reconstruction Working Group has developed the HMP Unified Metabolic Analysis Network (HUMAnN). The HUMAnN pipeline infers community function directly from short mWGS reads, using the KEGG ortholog (KO) groups. See the SOP or download page below for more information on using HUMAnN.
HUMAnN was run using Illumina reads from 743 samples as input. For each sample,
we provide the following files, as well as concatenated summary files
containing all sample output:
a) coverage files - presence or absence of each KEGG module/pathway in the community
b) abundance files - abundance of each KEGG module/pathway, ie how many copies of the module/pathway are present in the community
Also available is an Enzyme abundance file, providing metadata as well as abundance of every KEGG ortholog (KO) analyzed across each sample.
If you're interested in joint analysis of 16S and shotgun metagenomic datasets from the HMP, pairing up data from the same microbiome samples can initially seem tricky. The HMP Sample Flow Schematic indicates how these sample IDs are related experimentally, and provides tables joining 16S dataset "SN" and "PSN" identifiers with metagenomic dataset "SRS" identifiers.
Protocols and Tools