1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
2Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000166. Epub 2018 Mar 15.
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.
基于基因的方法在细菌基因组流行病学和暴发检测中越来越受欢迎。然而，对于这些方法，缺乏用于模式定义和等位基因调用的开源可扩展软件。chewBBACA 套件旨在帮助用户创建和评估新型全基因组或核心基因组基于基因的分型模式，并对感兴趣的细菌菌株进行随后的等位基因调用。chewBBACA 在从头组装器生成的完整或草图基因组上执行模式创建和等位基因调用。chewBBACA 软件使用 Python 3.4 或更高版本，可以在笔记本电脑或高性能集群上运行，因此对于小型实验室和大型参考中心都非常有用。chewBBACA 可在 https://github.com/B-UMMI/chewBBACA 上获得。
