chewbbaca
Link to section 'Introduction' of 'chewbbaca' Introduction
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 resulting from de novo assemblers.
BioContainers: https://biocontainers.pro/tools/chewbbaca
Home page: https://github.com/B-UMMI/chewBBACA
Link to section 'Versions' of 'chewbbaca' Versions
- 2.8.5
Link to section 'Commands' of 'chewbbaca' Commands
- chewBBACA.py
Link to section 'Module' of 'chewbbaca' Module
You can load the modules by:
module load biocontainers
module load chewbbaca
Link to section 'Example job' of 'chewbbaca' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run chewbbaca on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=chewbbaca
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers chewbbaca
chewBBACA.py CreateSchema -i complete_genomes/ -o tutorial_schema --ptf Streptococcus_agalactiae.trn --cpu 4
chewBBACA.py AlleleCall -i complete_genomes/ -g tutorial_schema/schema_seed -o results32_wgMLST --cpu 4