StrainFLAIR

Strain-level profiling of metagenomic samples using variation graphs. StrainFLAIR (STRAIN-level proFiLing using vArIation gRaph) is a tool for strain identification and quantification that uses variation graph representation of genes sequences. StrainFLAIR is sub-divided into two main parts: first, an indexing step that stores clusters of reference genes into variation graphs, and then, a query step using mapping of metagenomic reads to infere strain-level abundances in the queried sample. The input for indexation is a collection of complete genomes, draft genomes or metagenome-assembled genomes from which genes will be predicted. The input for query is the so-created graph and any read file.