| name | humann |
| description | Gene-family and pathway abundance profiling from metagenomes. Use this skill when working with humann: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/biobakery/humann. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["function","pathways","profiling"] |
| upstream | https://github.com/biobakery/humann |
HUMAnN
Upstream: biobakery/humann
Citation
Beghini, F. et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10, e65088 (2021). https://doi.org/10.7554/eLife.65088
See also docs/references.md.
Analytical thinking
HUMAnN maps reads to a gene catalog (UniRef-based) and aggregates to pathways.
Treat pathway abundance as homology-supported functional potential, not
measured enzyme activity or flux.
Prefer dehosted reads. HUMAnN commonly expects a single interleaved/merged PE
stream depending on version—follow the installed version’s input rules.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Input | Dehosted reads | From kneaddata |
| DBs | chocophlan + uniref | Version-locked with HUMAnN |
| RAM | 32 GB | 64–128 GB |
| Time | High | Parallelize by sample |
How to run
humann \
--input temp/hr/${id}_merged.fastq \
--output temp/humann/${id} \
--threads 8
Post-process: join tables, renormalize (CPM/RPK), regroup to KO/GO as needed.
Decision tree
Need functional pathways from reads?
├─ Yes → humann
├─ Only taxonomy → metaphlan or kraken2
└─ Gene catalogue on assemblies → prodigal + eggnog-mapper (+ salmon)
Related skills
metaphlan · kneaddata · visualization · eggnog-mapper
