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chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the crea...

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Detalles Bibliográficos
Autores principales: Silva, Mickael, Machado, Miguel P., Silva, Diogo N., Rossi, Mirko, Moran-Gilad, Jacob, Santos, Sergio, Ramirez, Mario, Carriço, João André
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885018/
https://www.ncbi.nlm.nih.gov/pubmed/29543149
http://dx.doi.org/10.1099/mgen.0.000166
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author Silva, Mickael
Machado, Miguel P.
Silva, Diogo N.
Rossi, Mirko
Moran-Gilad, Jacob
Santos, Sergio
Ramirez, Mario
Carriço, João André
author_facet Silva, Mickael
Machado, Miguel P.
Silva, Diogo N.
Rossi, Mirko
Moran-Gilad, Jacob
Santos, Sergio
Ramirez, Mario
Carriço, João André
author_sort Silva, Mickael
collection PubMed
description Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.
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spelling pubmed-58850182018-04-05 chewBBACA: A complete suite for gene-by-gene schema creation and strain identification Silva, Mickael Machado, Miguel P. Silva, Diogo N. Rossi, Mirko Moran-Gilad, Jacob Santos, Sergio Ramirez, Mario Carriço, João André Microb Genom Methods Paper Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA. Microbiology Society 2018-03-15 /pmc/articles/PMC5885018/ /pubmed/29543149 http://dx.doi.org/10.1099/mgen.0.000166 Text en © 2018 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.
spellingShingle Methods Paper
Silva, Mickael
Machado, Miguel P.
Silva, Diogo N.
Rossi, Mirko
Moran-Gilad, Jacob
Santos, Sergio
Ramirez, Mario
Carriço, João André
chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title_full chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title_fullStr chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title_full_unstemmed chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title_short chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
title_sort chewbbaca: a complete suite for gene-by-gene schema creation and strain identification
topic Methods Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885018/
https://www.ncbi.nlm.nih.gov/pubmed/29543149
http://dx.doi.org/10.1099/mgen.0.000166
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