HUMAnN2

HUMAnN2 profiles the functional potential and activity of microbial communities from metagenomic and metatranscriptomic short-read sequencing data, quantifying gene families and metabolic pathways with species-level resolution.

Key Features:

• Tiered search strategy: Implements a tiered search strategy that maps reads to species pangenomes before performing translated searches on unclassified reads to improve speed and specificity.
• Species identification: Identifies known species present in the microbial community.
• Pangenome alignment: Aligns reads against the pangenomes of identified species.
• Translated search on unclassified reads: Performs translated (protein-level) searches on reads that remain unclassified after pangenome alignment.
• Gene family and pathway quantification: Quantifies gene families and metabolic pathways to define functional potential and activity.
• Species-resolved profiling: Resolves gene family and pathway abundances to individual species within the community.
• Improved accuracy versus translated-only methods: Enhances accuracy of gene family profiles and accelerates profiling compared to pure translated search approaches.
• Support for sequencing reads: Operates on metagenomic and metatranscriptomic short DNA/RNA reads.
• Contributional diversity: Introduces the concept of "contributional diversity" to assess taxonomic contributions to pathway-level functions.

Scientific Applications:

• Marine metabolism clinal variation: Used to study clinal variation in marine metabolism.
• Human microbiome pathway contributions: Analyzes ecological contribution patterns among human microbiome pathways.
• Genomic versus transcriptional contributions: Investigates differences between genomic and transcriptional contributions of different species.
• Strain profiling: Enables strain profiling within microbial communities.
• Ecological assembly analysis: Explores patterns of ecological assembly across diverse microbial community types using contributional diversity.

Methodology:

Uses a tiered computational workflow of species identification, alignment of reads to species pangenomes, translated searches on unclassified reads, and quantification of gene families and metabolic pathways.