HUMAnN: The HMP Unified Metabolic Analysis Network. HUMAnN is a pipeline for efficiently and accurately determining the presence/absence and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. HUMAnN takes these reads as inputs and produces gene and pathway summaries as outputs: The abundance of each orthologous gene family in the community. Orthologous families are groups of genes that perform roughly the same biological roles. HUMAnN uses the KEGG Orthology (KO) by default, but any catalog of orthologs can be employed with minor changes (COG, NOG, etc.) The presence/absence of each pathway in the community. HUMAnN refers to pathway presence/absence as ”coverage,” and defines a pathway as a set of two or more genes. HUMAnN uses KEGG pathways and modules by default, but again can easily be modified to use GO terms or other gene sets. The abundance of each pathway in the community, i.e. how many ”copies” of that pathway are present.

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  1. Aßhauer, Kathrin Petra; Meinicke, Peter: On the estimation of metabolic profiles in metagenomics (2013)