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BlastFrost : fast querying of 100,000s of bacterial genomes in Bifrost graphs

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Luhmann, Nina, Holley, Guillaume and Achtman, Mark (2021) BlastFrost : fast querying of 100,000s of bacterial genomes in Bifrost graphs. Genome Biology, 22 . 30. doi:10.1186/s13059-020-02237-3

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Official URL: http://dx.doi.org/10.1186/s13059-020-02237-3

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Abstract

BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. We show two examples using Salmonella genomes, finding within minutes the presence of genes in the SPI-2 pathogenicity island in a collection of 926 genomes; and identifying single nucleotide polymorphisms associated with fluoroquinolone resistance in three genes among 190, 209 genomes. BlastFrost is available at https://github.com/nluhmann/BlastFrost.

Item Type: Journal Article
Subjects: H Social Sciences > HF Commerce
R Medicine > RB Pathology
T Technology > T Technology (General)
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Bacterial genomes, Charts, diagrams, etc., Workflow -- Computer programs
Journal or Publication Title: Genome Biology
Publisher: BioMed Central Ltd.
ISSN: 1474-7596
Official Date: 11 January 2021
Dates:
DateEvent
11 January 2021Published
5 December 2020Accepted
Date of first compliant deposit: 14 December 2020
Volume: 22
Article Number: 30
DOI: 10.1186/s13059-020-02237-3
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
202792/Z/16/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
152399-053Icelandic Centre for Researchhttp://dx.doi.org/10.13039/501100001840
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