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

Area of Science:

• Genomic epidemiology
• Bioinformatics
• Microbial genomics

Background:

• Gene-by-gene typing methods are increasingly vital for bacterial genomic epidemiology and outbreak detection.
• Existing methodologies lack scalable, open-source software for schema definition and allele calling.
• This gap hinders efficient and reproducible bacterial strain analysis.

Purpose of the Study:

• To introduce chewBBACA, an open-source software suite for bacterial gene-by-gene typing.
• To facilitate the creation and evaluation of whole-genome and core-genome typing schemas.
• To enable accurate allele calling in bacterial strains.

Main Methods:

• chewBBACA performs schema creation and allele calling using Python 3.4+.
• The software analyzes complete or draft bacterial genomes from de novo assemblers.
• It is designed for scalability on laptops and high-performance computing clusters.

Main Results:

• chewBBACA provides a robust solution for defining and applying gene-by-gene typing schemas.
• The software enables accurate allele calling, crucial for epidemiological studies.
• Its scalability supports diverse laboratory settings, from small labs to large reference centers.

Conclusions:

• chewBBACA addresses the need for open-source, scalable software in bacterial gene-by-gene typing.
• The suite enhances bacterial genomic epidemiology and outbreak detection capabilities.
• It offers a valuable tool for researchers and public health professionals worldwide.