chewBBACA stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow" but at this point it still needs a bit of work to make that claim, so we just add "chew" to add extra coolness to the software name. BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.
chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes.
Check the documentation for implementation details and guidance on using chewBBACA.
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Changed FASTA file validation to reduce memory usage.
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Removed legacy schema conversion. Users should use the
PrepExternalSchemamodule to adapt schemas created with chewBBACA<=2.1.0. -
Added prints about output files created by the
PrepExternalSchemamodule.
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