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exercises/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
+        /shares/amr.imm.uzh/bioinfo/singularity/abricate_1.0.1--ha8f3691_1.sif
+        abricate --list
+
+### 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]`
+
+    Use the databases `ncbi` and `vfdb`
+
+    The Singularity image can be found at
+
+        /shares/amr.imm.uzh/bioinfo/singularity7quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img
+
+    Use 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