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

Mickael Silva; Miguel P. Machado; Diogo N. Silva; Mirko Rossi; Jacob Moran-Gilad; Sergio Santos; Mario Ramirez; João André Carriço

doi:https://doi.org/10.1099/mgen.0.000166

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

Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, João André Carriço

Department of Health Policy and Management

Ben-Gurion University of the Negev

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	American English
Journal	Microbial Genomics
Volume	4
Issue number	3
DOIs	https://doi.org/10.1099/mgen.0.000166
State	Published - 1 Mar 2018

Keywords

allele calling
chewBBACA
gene-by-gene
multilocus sequence typing
schema

All Science Journal Classification (ASJC) codes

Genetics
Molecular Biology
Epidemiology
Microbiology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

https://doi.org/10.1099/mgen.0.000166

Cite this

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title = "chewBBACA: A complete suite for gene-by-gene schema creation and strain identification",

abstract = "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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author = "Mickael Silva and Machado, {Miguel P.} and Silva, {Diogo N.} and Mirko Rossi and Jacob Moran-Gilad and Sergio Santos and Mario Ramirez and Carri{\c c}o, {Jo{\~a}o Andr{\'e}}",

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doi = "https://doi.org/10.1099/mgen.0.000166",

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AU - Silva, Diogo N.

AU - Rossi, Mirko

AU - Moran-Gilad, Jacob

AU - Santos, Sergio

AU - Ramirez, Mario

AU - Carriço, João André

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

Abstract

Keywords

All Science Journal Classification (ASJC) codes

UN SDGs

Access to Document

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