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humann-functional-profiler skill

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This skill provides HUMAnN functional profiling for metagenomic pathway analysis, quantifying gene families, pathways, and annotations to inform microbial

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SKILL.md

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---
name: humann-functional-profiler
description: HUMAnN functional profiling skill for metagenomic pathway analysis
allowed-tools:
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metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - metagenomics
    - functional
    - pathway
    - metabolism
---

# HUMAnN Functional Profiler Skill

## Purpose
Provide HUMAnN functional profiling for metagenomic pathway analysis.

## Capabilities
- Gene family quantification
- MetaCyc pathway abundance
- UniRef annotation
- Stratified functional profiles
- Pathway coverage analysis
- Custom database integration

## Usage Guidelines
- Run taxonomic profiling first
- Quantify gene families and pathways
- Stratify by organism when relevant
- Analyze pathway coverage
- Compare functional profiles
- Document database versions

## Dependencies
- HUMAnN3
- eggNOG-mapper
- Prokka

## Process Integration
- Shotgun Metagenomics Pipeline (shotgun-metagenomics)

Overview

This skill provides HUMAnN-based functional profiling tailored for metagenomic pathway analysis. It automates gene family quantification, pathway abundance estimation, and stratified functional profiles to reveal community-level metabolic potential. The skill supports custom databases and produces pathway coverage metrics for downstream comparison and visualization.

How this skill works

The skill runs HUMAnN3 workflows to map reads to UniRef gene families, quantify gene family abundance, and reconstruct MetaCyc pathway abundances. It can stratify results by contributing taxa and compute pathway coverage to distinguish presence from activity. Integration points allow using outputs from taxonomic profiling and feeding results into downstream pipelines or comparative analyses.

When to use it

After completing taxonomic profiling of shotgun metagenomes
When you need quantitative gene family and pathway abundance estimates
To obtain stratified functional profiles by organism
When comparing metabolic potential across samples or conditions
When validating pathway completeness via coverage analysis

Best practices

Run a taxonomic profiling step first to improve mapping specificity
Document database versions (UniRef, MetaCyc, custom DBs) for reproducibility
Use stratification to link functions to taxa before interpreting ecological roles
Validate key findings with complementary tools (e.g., Prokka annotations or eggNOG-mapper)
Keep intermediate files and logs to facilitate re-run and troubleshooting

Example use cases

Quantify gene family abundance across environmental or clinical metagenomes
Compare MetaCyc pathway abundances between treatment and control cohorts
Identify organisms that contribute to specific metabolic pathways using stratified profiles
Assess pathway completeness and coverage to prioritize experimentally testable hypotheses
Integrate HUMAnN outputs into larger shotgun metagenomics pipelines for automated reporting

FAQ

Do I need to run taxonomic profiling first?

Yes. Running a taxonomic profiling step before HUMAnN improves mapping accuracy and enables meaningful stratification by organism.

Can I use custom databases?

Yes. The skill supports custom database integration, but you should record database versions and ensure compatibility with HUMAnN3 formats.