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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
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 | |||||||||
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| Subjects: | H Social Sciences > HF Commerce R Medicine > RB Pathology T Technology > T Technology (General) |
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| 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 |
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| 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 | |||||||||
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| 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 | |||||||||
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