ncbi-amrfinderplus
Link to section 'Introduction' of 'ncbi-amrfinderplus' Introduction
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.
BioContainers: https://biocontainers.pro/tools/ncbi-amrfinderplus
Home page: https://github.com/ncbi/amr
Link to section 'Versions' of 'ncbi-amrfinderplus' Versions
- 3.10.30
- 3.10.42
Link to section 'Commands' of 'ncbi-amrfinderplus' Commands
- amrfinder
Link to section 'Module' of 'ncbi-amrfinderplus' 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 If you notice our database is out of date, you can contact us to update the database.
Link to section 'Example job' of 'ncbi-amrfinderplus' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
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