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.
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Added support for genetic codes 2, 3, 5, 6, 9, 10, 12-16, 21-25 (complete list available here). Values passed to
--t,--translation-tableare ignored if a training file is used. The CreateSchema, AlleleCall and PrepExternalSchema modules use the genetic code used to create the training file. -
Fixed issue related to data about CDSs close to the contig tips not being available if input FASTA files contain CDSs and
--cdsis used. -
Fixed issue in the AlleleCallEvaluator module related to entirely numeric columns.
Check our Changelog to learn about the latest changes.
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