A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events.

ABSTRACT: Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular

SUBMITTER: Jaillard M 

PROVIDER: S-EPMC6258240 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature