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AMR
Blockkurs MicrobialBioinfo
Commits
54688ca7
Commit
54688ca7
authored
11 months ago
by
Tim Roloff Handschin
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Update abricate_exercise.md
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exercises/abricate_exercise.md
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@@ -6,7 +6,7 @@
<https://github.com/tseemann/abricate>
### Check for available databases
### Check for available databases
in an interactive session
-
Abricate can search various databases (even custom built).
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@@ -14,7 +14,7 @@
srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l
module load singularityce
srun /shares/amr.imm.uzh/bioinfo/singularity/
quay.io-biocontainers-
abricate
-
1.0.1
--ha8f3691_1.img
abricate --list
srun /shares/amr.imm.uzh/bioinfo/singularity/
sandbox/
abricate
_
1.0.1 abricate --list
-
This will generate the following output
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@@ -29,6 +29,8 @@
ecoli_vf 2701 nucl 2021-Mar-27
vfdb 2597 nucl 2021-Mar-27
-
**Close your interactive session**
before you continue
### Screen your genomes for resistance genes and virulence factors
-
**How to run abricate:**
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