diff --git a/exercises/abricate_exercise.md b/exercises/abricate_exercise.md index 18ab12408d00eda35339fe1b082befe9adccda45..697efa29fb9ee21e6f187f06c074fa6914a58cbf 100644 --- a/exercises/abricate_exercise.md +++ b/exercises/abricate_exercise.md @@ -10,13 +10,15 @@ - 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: +- 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 + 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 @@ -44,3 +46,6 @@ #SBATCH --job-name=abricate #SBATCH --output=abricate\_%A\_%a.out #SBATCH --error=abricate\_%A\_%a.err + +- **Supplement:** + Screen for plasmids as well