From b74044eb4a96f76fe85d86ccf0dd5195ee23fda2 Mon Sep 17 00:00:00 2001
From: Tim Roloff Handschin <troloff@imm.uzh.ch>
Date: Thu, 30 Mar 2023 21:15:29 +0200
Subject: [PATCH] Replace abricate_exercise.md
---
exercises/abricate_exercise.md | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/exercises/abricate_exercise.md b/exercises/abricate_exercise.md
index 18ab124..697efa2 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
--
GitLab