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

Holley, Guillaume; Melsted, Páll

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dc.contributor	Háskóli Íslands
dc.contributor	University of Iceland
dc.contributor.author	Holley, Guillaume
dc.contributor.author	orcid.org/0000-0002-8418-6724 Melsted, Páll
dc.date.accessioned	2020-11-09T15:47:21Z
dc.date.available	2020-11-09T15:47:21Z
dc.date.issued	2020-09-17
dc.identifier.citation	Holley, 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/s13059-020-02135-8
dc.identifier.issn	1474-760X
dc.identifier.uri	https://hdl.handle.net/20.500.11815/2193
dc.description	Publisher's version (útgefin grein)
dc.description.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
dc.description.sponsorship	This work was supported by the Icelandic Research Fund Project grant number 152399-053.
dc.format.extent	249
dc.language.iso	en
dc.publisher	Springer Science and Business Media LLC
dc.relation.ispartofseries	Genome Biology;21(1)
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	de Bruijn graphs
dc.subject	Memory
dc.subject	Erfðafræði
dc.subject	Genamengi
dc.subject	Línurit
dc.title	Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
dc.type	info:eu-repo/semantics/article
dcterms.license	Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
dc.description.version	Peer Reviewed
dc.identifier.journal	Genome Biology
dc.identifier.doi	10.1186/s13059-020-02135-8
dc.relation.url	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02135-8
dc.contributor.department	Iðnaðarverkfræði-, vélaverkfræði- og tölvunarfræðideild (HÍ)
dc.contributor.department	Faculty of Industrial Eng., Mechanical Eng. and Computer Science (UI)
dc.contributor.school	Verkfræði- og náttúruvísindasvið (HÍ)
dc.contributor.school	School of Engineering and Natural Sciences (UI)