Overview

About chewBBACA

chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The “BBACA” stands for “BSR-Based Allele Calling Algorithm”. BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.. The “chew” part adds extra coolness to the name and could be thought of as “Comprehensive and Highly Efficient Workflow”. chewBBACA allows to define the target loci in a schema based on multiple genomes (e.g. define target loci based on the distinct loci identified in a dataset of high-quality genomes for a species or lineage of interest) and performs allele calling to determine the allelic profiles of bacterial strains, easily scaling to thousands of genomes with modest computational resources. chewBBACA includes functionalities to annotate the schema loci, compute the set of loci that constitute the core genome for a given dataset, and generate interactive reports for schema and allele calling results evaluation to enable an intuitive analysis of the results in surveillance and outbreak detection settings or population studies. Pre-defined cg/wgMLST schemas can be downloaded from Chewie-NS or adapted from other cg/wgMLST platforms.

The general workflow of chewBBACA is represented in the following image:

Citation

chewBBACA has been published (version 2.0.5 at the time) in Microbial Genomics under the title: chewBBACA: A complete suite for gene-by-gene schema creation and strain identification - Link to paper.

When using chewBBACA please use the following citation:

Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:000166. doi:10.1099/mgen.0.000166

Licensing

This project is licensed under the GPLv3 license. The source code of chewBBACA is available at https://github.com/B-UMMI/chewBBACA.

Funding

INNUENDO project co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 (“New approaches in identifying and characterizing microbial and chemical hazards”). The conclusions, findings, and opinions expressed in this review paper reflect only the view of the authors and not the official position of the European Food Safety Authority (EFSA).
ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento” from “Programa Operacional Regional Lisboa 2020” FCT - “Fundação para a Ciência e a Tecnologia”.
BacGenTrack (TUBITAK/0004/2014) [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBİTAK)]