HUMAnN2 is the second generation of HUMAnN (HMP Unified Metabolic Analysis Network). It is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomatic sequencing data, produced by the Huttenhower lab at Harvard.
- HUMAnN2 web home
- The bioBakery tools and tutorials wiki, which provides software, documentation, and tutorials for methods for microbial community profiling developed by the Huttenhower lab.
- Citation: If you use HUMAnN2 in your work, please cite:
- Franzosa EA*, McIver LJ*, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 15: 962-968 (2018).
To see what versions of HUMAnN2 are available type
module avail humann2
To see what other modules are needed, what commands are available and how to get additional help type
module help humann2
To use HUMAnN2, include a command like this in your batch script or interactive session to load the humann2 module:
module load humann2
Be sure you also load any other modules needed, as listed by the
module help humann2 command.