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bio-metagenomics-functional-profiling
Maintainer FreedomIntelligence · Last updated April 1, 2026
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-functional-profiling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: humann --input reads.fastq --output results/ (HUMAnN3).
- What metabolic pathways are present in my metagenome?" → Profile functional potential of metagenomic samples to obtain pathway abundances and gene family counts using translated search against UniRef and MetaCyc. CLI: humann --input reads.fastq --output results/ (HUMAnN3).
- Profile the functional potential of metagenomic samples using HUMAnN3 to get pathway and gene family abundances.
- conda create -n humann -c bioconda humann conda activate humann.
Source Doc
Excerpt From SKILL.md
Download databases
humann_databases --download chocophlan full /path/to/databases humann_databases --download uniref uniref90_diamond /path/to/databases
Update config with database paths
humann_config --update database_folders nucleotide /path/to/databases/chocophlan humann_config --update database_folders protein /path/to/databases/uniref
## Run HUMAnN3 on a single sample
humann --input sample.fastq.gz --output sample_humann
Use cases
- Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- metagenomics/metaphlan-profiling - Taxonomic profiling (input for HUMAnN)
- metagenomics/kraken-classification - Alternative taxonomy
- metagenomics/metagenome-visualization - Visualization methods
- pathway-analysis/kegg-pathways - KEGG pathway interpretation
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