Humann Functional Profiler

---
name: humann-functional-profiler
description: HUMAnN functional profiling skill for metagenomic pathway analysis
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - metagenomics
    - functional
    - pathway
    - metabolism
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:statistical-analysis, skill-area:graph-algorithms, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer, role:biomedical-engineer]
---

# 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)