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.
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.