TY - JOUR T1 - chewBBACA: A complete suite for gene-bygene schema creation and strain identification JF - bioRxiv DO - 10.1101/173146 SP - 173146 AU - Mickael Silva AU - Miguel Machado AU - Mirko Rossi AU - Jacob Moran-Gilad AU - Sergio Santos AU - Mario Ramirez AU - João André Carriço Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/08/08/173146.abstract N2 - 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/Contact jcarrico{at}fm.ul.ptSupplementary information Supplementary data are available at https://github.com/B-UMMI/chewBBACA/wiki ER -