GitHub - B-UMMI/chewBBACA: BSR-Based Allele Calling Algorithm (original) (raw)

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

3.5.4 - 2026-04-22

This release adds the following bug fixes:

• The file with the cgMLST MSA was missing from the output directory created by the AlleleCallEvaluator module since the release of the ComputeMSA module (thanks to @victor5lm who reported this issue in #235). This change was unintended. The file with cgMLST MSA was re-added as one of the output files from the AlleleCallEvaluator module (protein_msa.fasta file). Simplified the conditions used to determine which steps to run.
• Made the definition of the sequence headers for the adapted schemas created by the PrepExternalSchema less rigid to better deal with unexpected headers. Added tests to validate schema adaptation for multiple external schema formats (e.g., EnteroBase, PubMLST, and Ridom).
• Fixed the parsing of the file with loci annotations in the LoadSchema module.
• Fixed the creation of the paths to intermediate FASTA files used by BLASTp to determine representative alleles during schema adaptation. The paths were not properly created when the SyncSchema module called the PrepExternalSchema module using relative paths.
• Changed the index value used by the select_highest_scores function to sort and select the highest scoring BLASTp matches per target from 5 to 6. The results were being sorted based on the length of the target sequences instead of the alignment raw score. This issue would not allow to identify the best scoring alignment in some cases, potentially leading to some sequences not being classified if a lower scoring alignment was selected. Fixing this issue results in a slight increase in the accuracy of the allele calling (thanks to @andreaderuvo for reporting this issue in #234).

Check our Changelog to learn more about the latest changes.

Citation

If you use chewBBACA, please cite the following publication:

Mamede R, Vila-Cerqueira P, Carriço JA, Ramirez M. 2026. chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing. Genome Med 18:51. https://doi.org/10.1186/s13073-026-01625-x

The supplementary material for the publication is available on Zenodo.

Other relevant citations:

• chewBBACA's first publication (if using a version < 2.1.0):

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. https://doi.org/10.1099/mgen.0.000166

• Chewie-NS (if using any of the schemas deposited on Chewie-NS):

Mamede R, Vila-Cerqueira P, Silva M, Carriço JA, Ramirez M. 2021. Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. Nucleic Acids Res 49:D660–D666. https://doi.org/10.1093/nar/gkaa889

Please consider also citing the awesome software dependencies used by chewBBACA. The full list of dependencies is available here.