chewBBACA 3.5.3

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

chewBBACA

chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm". BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.. The "chew" part adds extra coolness to the name and could be thought of as "Comprehensive and Highly Efficient Workflow". chewBBACA allows to define the target loci in a schema based on multiple genomes (e.g. define target loci based on the distinct loci identified in a dataset of high-quality genomes for a species or lineage of interest) and performs allele calling to determine the allelic profiles of bacterial strains, easily scaling to thousands of genomes with modest computational resources. chewBBACA includes functionalities to annotate the schema loci, compute the set of loci that constitute the core genome for a given dataset, and generate interactive reports for schema and allele calling results evaluation to enable an intuitive analysis of the results in surveillance and outbreak detection settings or population studies. Pre-defined cg/wgMLST schemas can be downloaded from Chewie-NS or adapted from other cg/wgMLST platforms.

Check the documentation for implementation details and guidance on using chewBBACA.

News

3.5.3 - 2026-03-10

• Fixed issue on the PrepExternalSchema module related to reading empty FASTA files after attempting to translate FASTA files from external schemas that contained no valid alleles. This issue did not affect the end result because the PrepExternalSchema module would detect that no alleles could be translated, skipping the next steps for that locus. However, not reading empty FASTA files avoids a warning raised by Biopython that could lead to errors in future releases.

• Add support for more recent versions of Numpy, SciPy, and Pandas (the versions of these dependencies were fixed to older versions due to past issues installing Pandas).

• Drop support for Python<=3.9. chewBBACA now requires Python>=3.10.

Check our Changelog to learn about the latest changes.

Citation

When using chewBBACA, please use the following citation:

Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:000166. doi:10.1099/mgen.0.000166