## 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