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HUMAnN3 Specifications

Process Details

  • Name: HUMAnN3
  • Process UUID: f931n87ll8yzawx6qlt36pgif8y352
  • Process Group: Functional Profiling

Overview

HUMAnN3 is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question "What are the microbes in my community-of-interest doing (or capable of doing)?"

This process is implemented in Bash, which utilizes the HUMAnN3 bioinformatics pipeline for comprehensive functional profiling analysis.

Key Functionality

  • Functional Profiling: Profiles the presence/absence and abundance of microbial pathways from metagenomic or metatranscriptomic sequencing data
  • Metabolic Potential Assessment: Describes the metabolic capabilities of microbial communities and their individual members
  • Multi-Database Integration: Integrates ChocoPhlAn, UniRef, and MetaPhlAn databases for comprehensive pathway annotation
  • High-Throughput Processing: Efficiently processes millions of short DNA/RNA reads with multi-threading support

Input/Output Specification

Inputs

Required Inputs

  • Sequencing Reads

    • Description: Metagenomic or metatranscriptomic sequencing data containing millions of short DNA/RNA reads
    • Format: FASTQ

  • MetaPhlAn Database

    • Description: Database for taxonomic profiling of microbial communities
    • Format: MetaPhlAn

  • ChocoPhlAn Database

    • Description: Nucleotide database containing species-level pangenome sequences for pathway annotation
    • Format: ChocoPhlAn

  • UniRef Database

    • Description: Protein database for functional annotation of unclassified reads
    • Format: UniRef

Outputs

  • Pathway Abundance Tables
    • Description: Tab-separated files containing microbial pathway presence/absence and abundance profiles
    • Format: TSV

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Run HUMAnN exclusively?
    • Description: This option runs metaphlan once more taking that much more time and resource, but since HUMAnN doesn't support more recent versions of MetaPhlAn, this, currently is necessary.
    • Available options: yes (default), no

References & Resources

  • Tool Documentation: Contact the team for details on HUMAnN3 implementation
  • Related Papers: Beghini, F., McIver, L.J., Blanco-Míguez, A., et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 2021;10:e65088. DOI: 10.7554/eLife.65088