Háskóli ÍslandsUniversity of IcelandHolley, GuillaumeMelsted, Páll2020-11-092020-11-092020-09-17Holley, G., Melsted, P. Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs. Genome Biology 21, 249 (2020). https://doi.org/10.1186/s13059-020-02135-81474-760Xhttps://hdl.handle.net/20.500.11815/2193Publisher's version (útgefin grein)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, editing, 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/bifrost249eninfo:eu-repo/semantics/openAccessde Bruijn graphsMemoryErfðafræðiGenamengiLínuritinfo:eu-repo/semantics/articleGenome Biology10.1186/s13059-020-02135-8