RT Journal Article SR Electronic T1 chewBBACA: A complete suite for gene-bygene schema creation and strain identification JF bioRxiv FD Cold Spring Harbor Laboratory SP 173146 DO 10.1101/173146 A1 Mickael Silva A1 Miguel Machado A1 Mirko Rossi A1 Jacob Moran-Gilad A1 Sergio Santos A1 Mario Ramirez A1 João André Carriço YR 2017 UL http://biorxiv.org/content/early/2017/08/08/173146.abstract AB 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