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

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 identificatio...

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Detalles Bibliográficos
Autores principales: Luhmann, Nina, Holley, Guillaume, Achtman, Mark
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7798312/
https://www.ncbi.nlm.nih.gov/pubmed/33430919
http://dx.doi.org/10.1186/s13059-020-02237-3
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author Luhmann, Nina
Holley, Guillaume
Achtman, Mark
author_facet Luhmann, Nina
Holley, Guillaume
Achtman, Mark
author_sort Luhmann, Nina
collection PubMed
description 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/tree/master/data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-020-02237-3).
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spelling pubmed-77983122021-01-12 BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs Luhmann, Nina Holley, Guillaume Achtman, Mark Genome Biol Method 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/tree/master/data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-020-02237-3). BioMed Central 2021-01-11 /pmc/articles/PMC7798312/ /pubmed/33430919 http://dx.doi.org/10.1186/s13059-020-02237-3 Text en © The Author(s) 2021 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.
spellingShingle Method
Luhmann, Nina
Holley, Guillaume
Achtman, Mark
BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title_full BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title_fullStr BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title_full_unstemmed BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title_short BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
title_sort blastfrost: fast querying of 100,000s of bacterial genomes in bifrost graphs
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7798312/
https://www.ncbi.nlm.nih.gov/pubmed/33430919
http://dx.doi.org/10.1186/s13059-020-02237-3
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