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chewbbaca

Description

chewbbaca website

chewBBACA “BSR-Based Allele Calling Algorithm” 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 for schema and results evaluation. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers.

Environment Modules

Run module spider chewbbaca to find out what environment modules are available for this application.

Environment Variables

  • HPC_CHEWBACCA_DIR - installation directory
  • HPC_CHEWBACCA_BIN - executable directory

Additional Usage Information

After loading the module, run the following command to display the help message:

$ chewbbaca -h

Citation

If you publish research that uses chewbbaca you have to cite it as follows:

Silva, M., Machado, M. P., Silva, D. N., Rossi, M., Moran‑Gilad, J., Santos, S., Ramirez, M., & Carriço, J. A. (2018, March 15). chewBBACA: A complete suite for gene‑by‑gene schema creation and strain identification. Microbial Genomics, 4(3), e000166. https://doi.org/10.1099/mgen.0.000166

Categories

biology, genomics