Graphite: painting genomes using a colored De Bruijn graph

Abstract

AbstractThe recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored De Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length. By focusing on the closest genomic match of each query region, Graphite reduces the number of matches while providing promising leads for genomic forensics. When applied to hundreds ofCampylobactergenomes we found extensive gene sharing, including a previously undetectedC. coliplasmid that matched aC. jejunichromosome. Together, genome painting using cDBGs as enabled by Graphite, can reveal new biological phenomena by mitigating computational hurdles. Graphite is implemented in Julia, available athttps://github.com/MGXlab/Graphite.