abricate_exercise.md

Resistance and virulence gene search with abricate

• We will use the software abricate by Thorsten Seemann to screen our:

• More info on software can be found at:

  https://github.com/tseemann/abricate

Check for available databases

• Abricate can search various databases (even custom built).

• We can write a script to check which databases are installed and available using abricate --list We can also run that in an interactive session using the code below:

  srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l 
  module load singularityce
  srun /shares/amr.imm.uzh/bioinfo/singularity/abricate_1.0.1--ha8f3691_1.sif abricate --list

• This will generate the following output

  DATABASE SEQUENCES DBTYPE DATE card 2631 nucl 2021-Mar-27 resfinder 3077 nucl 2021-Mar-27 megares 6635 nucl 2021-Mar-27 ncbi 5386 nucl 2021-Mar-27 argannot 2223 nucl 2021-Mar-27 plasmidfinder 460 nucl 2021-Mar-27 ecoh 597 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27

Screen your genomes for resistance genes and virulence factors

• How to run abricate:

  Generate an array job script to feed in fasta assembly files you want to investigate to abricate

  abricate my_file.fasta

  Add the following parameters --quiet --nopath --db [DATABASE]

  Run abricate twice, once on ncbi and once vfdb

  The Singularity image can be found at

  /shares/amr.imm.uzh/bioinfo/singularity7quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img

  Use the following SLURM parameters:

  #!/usr/bin/env bash 
  #SBATCH --time=01:00:00 
  #SBATCH --array=0-7 
  #SBATCH --mem-per-cpu=10G 
  #SBATCH --cpus-per-task=8 
  #SBATCH --job-name=abricate 
  #SBATCH --output=abricate\_%A\_%a.out 
  #SBATCH --error=abricate\_%A\_%a.err

• Supplement: Screen for plasmids as well