chicken_pig_amr

Snakemake pipeline for assembly of chicken and pig AMR datasets

You will need

• Snakemake
• Conda

Practice run:

snakemake -np

Simple usage:

snakemake --use-conda 

Cluster usage:

snakemake --jobscript custombash.sh --use-conda --cluster-config cluster.json --cluster "qsub -R yes -V -S /bin/bash -cwd -pe sharedmem {cluster.core} -l h_rt={cluster.time} -l h_vmem={cluster.vmem} -P {cluster.proj}" --jobs 5000