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
3.5.4 - 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
AlleleCallEvaluatormodule since the release of theComputeMSAmodule (thanks to @victor5lm who reported this issue in https://github.com/B-UMMI/chewBBACA/issues/235). This change was unintended. The file with cgMLST MSA was re-added as one of the output files from theAlleleCallEvaluatormodule (protein_msa.fastafile). Simplified the conditions used to determine which steps to run. - Made the definition of the sequence headers for the adapted schemas created by the
PrepExternalSchemaless 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
LoadSchemamodule. - 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
SyncSchemamodule called thePrepExternalSchemamodule using relative paths. - Changed the index value used by the
select_highest_scoresfunction to sort and select the highest scoring BLASTp matches per target from5to6. 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 https://github.com/B-UMMI/chewBBACA/issues/234).
Check our Changelog to learn more 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
5 maintainers
Metadata
5 maintainers
Release files for chewBBACA 3.5.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| chewbbaca-3.5.4.tar.gz | 10.9 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| chewbbaca-3.5.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 21.9 MB
Release files / chewbbaca-3.5.4.tar.gz
| Download URL | chewbbaca-3.5.4.tar.gz |
|---|---|
| Size | 10.9 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / chewbbaca-3.5.4-py3-none-any.whl
| Download URL | chewbbaca-3.5.4-py3-none-any.whl |
|---|---|
| Size | 11.0 MB |
| Tags | Python 3 |
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No |
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twine/6.2.0 CPython/3.10.13
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