chewBBACA 3.3.6

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

3.3.6 - 2024-06-12

• Added support for translation tables different than 11 to UniprotFinder and AlleleCallEvaluator.

• Added check for legacy schemas that include files terminating in bsr.txt. The AlleleCall module warns users that the schema needs to be adapted and exits.

• Changed the max_targets value in UniprotFinder to avoid BLASTp warning when aligning schema representative alleles against proteomes.

• Fixed an issue in the AlleleCallEvaluator module when using --no-pa and --no-dm.

• The AlleleCallEvaluator module no longer tries to compute the distance matrix, MSA, and tree if the cgMLST is composed of 0 loci.

• Fixed an issue in RemoveGenes where it would not get the first ID in the input list.

• Updated Dockerfile. Using pip to install chewBBACA instead of downloading source from GitHub.

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