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


ABSTRACT: 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/bifrost.

SUBMITTER: Holley G 

PROVIDER: S-EPMC7499882 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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

Holley Guillaume G   Melsted Páll P  

Genome biology 20200917 1


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, edi  ...[more]

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