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

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dc.contributor Háskóli Íslands
dc.contributor University of Iceland
dc.contributor.author Holley, Guillaume
dc.contributor.author 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)

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