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.

• Version: git-87102063 (this roughly corresponds to version 3.3.0)
• Added: September, 2023
• Link: https://github.com/B-UMMI/chewBBACA

See versions that are available:

$ module avail chewbbaca

Load one version into your environment and run it:

$ module load chewbbaca/git-87102063
$ chewie

Notes from the sysadmin during installation.

$ git clone https://github.com/B-UMMI/chewBBACA.git
$ sudo mkdir -p /export/apps/chewbbaca/git-87102063
$ sudo chown aorth /export/apps/chewbbaca/git-87102063
$ module load python/3.9
$ python3 -m venv /export/apps/chewbbaca/git-87102063/.venv
$ source /export/apps/chewbbaca/git-87102063/.venv/bin/activate
$ pip install --upgrade pip setuptools wheel
$ python3 setup.py install
$ sudo chown -R root:root /export/apps/chewbbaca/git-87102063

See the bioconda meta.yaml for chewbbaca for more information.