Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

Guillaume Holley, Páll Melsted
2020 Genome Biology  
Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing,
more » ... ting, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in.Availability https://github.com/pmelsted/bifrost.
doi:10.1186/s13059-020-02135-8 pmid:32943081 pmcid:PMC7499882 fatcat:dgrvnmstwrgenby6dcfjirbe3m