StrainFLAIR

StrainFLAIR performs strain-level identification and quantification in metagenomic samples by mapping metagenomic reads to variation (pangenome) graphs built from clusters of reference genes.

Key Features:

• Variation Graph Representation: Uses pangenome/variation graphs of gene clusters to represent multiple genomes and capture strain-level genetic variation.
• Two-Step Process (Indexing and Query): Indexes clusters of reference genes into variation graphs using complete genomes, draft genomes, or metagenome-assembled genomes, then maps metagenomic reads to those graphs to infer strain-level abundances.
• High Precision in Complex Environments: Distinguishes and estimates abundances of closely related strains within complex mixtures of bacterial species and strains.

Scientific Applications:

• Strain-level abundance profiling: Resolves abundances of individual strains within metagenomic samples for detailed community composition analysis.
• Characterization of unknown sequenced genomes: Compares unknown or newly sequenced genomes against graph-based references to identify strain membership and variation.
• Microbiome–phenotype association studies: Supports investigations of associations between specific bacterial strains and phenotypic traits relevant to health and disease.

Methodology:

Indexes clusters of reference genes into variation (pangenome) graphs from complete genomes, draft genomes, or metagenome-assembled genomes, then maps metagenomic reads against these graphs to identify and quantify strain-level variations and abundances.