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Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
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| Titill: | Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs |
| Höfundur: |
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| Útgáfa: | 2020-09-17 |
| Tungumál: | Enska |
| Umfang: | 249 |
| Háskóli/Stofnun: | Háskóli Íslands University of Iceland |
| Svið: | Verkfræði- og náttúruvísindasvið (HÍ) School of Engineering and Natural Sciences (UI) |
| Deild: | Iðnaðarverkfræði-, vélaverkfræði- og tölvunarfræðideild (HÍ) Faculty of Industrial Eng., Mechanical Eng. and Computer Science (UI) |
| Birtist í: | Genome Biology;21(1) |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-020-02135-8 |
| Efnisorð: | de Bruijn graphs; Memory; Erfðafræði; Genamengi; Línurit |
| URI: | https://hdl.handle.net/20.500.11815/2193 |
Tilvitnun: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
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Útdráttur: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
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Athugasemdir:Publisher's version (útgefin grein)
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Leyfi: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.
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