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

posted Aug 9, 2017, 6:36 AM by Mirko Rossi   [ updated Aug 9, 2017, 6:36 AM ]
Mickael Silva, Miguel P. Machado, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, Joao Andre Carrico
doi: https://doi.org/10.1101/173146

Motivation: Gene-by-gene (GbG) approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open source software for schema definition and allele calling. Results: The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome GbG schemas and allele calling in bacterial strains of interest. The alleles called by chewBBACA are potential coding sequences, allowing the user to evaluate the possible consequences of the observed diversity. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. Availability: https://github.com/B-UMMI/chewBBACA/.

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