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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
$ 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 install
$ sudo chown -R root:root /export/apps/chewbbaca/git-87102063

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

chewbbaca-software.txt · Last modified: 2023/09/28 09:59 by aorth