Software: Ncbi-amrfinderplus
Description
Ncbi-amrfinderplus and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa.
Available Versions
| Unspecified: | 3.10.30 3.10.42 3.11.2 |
|---|
BioContainers: https://biocontainers.pro/tools/ncbi-amrfinderplus
Home page: https://github.com/ncbi/amr
Commands
- amrfinder
Module
You can load the modules by:
module load biocontainers
module load ncbi-amrfinderplus
AMRFinderPlus database has been setup for users. Users can check the database version by amrfinder -V. RCAC will keep updating database for users. If you notice our database is out of date, you can contact us to update the database.
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run ncbi-amrfinderplus on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ncbi-amrfinderplus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ncbi-amrfinderplus
# Protein AMRFinder with no genomic coordinates
amrfinder -p test_prot.fa
# Translated nucleotide AMRFinder (will not use HMMs)
amrfinder -n test_dna.fa
# Protein AMRFinder using GFF to get genomic coordinates and 'plus' genes
amrfinder -p test_prot.fa -g test_prot.gff --plus
# Protein AMRFinder with Escherichia protein point mutations
amrfinder -p test_prot.fa -O Escherichia
# Full AMRFinderPlus search combining results
amrfinder -p test_prot.fa -g test_prot.gff -n test_dna.fa -O Escherichia --plus