====== AMRFinderPlus ======
This software 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. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

Note that AMRFinderPlus reports gene and point mutation presence/absence; it does not infer phenotypic resistance. Many of the resistance genes detected by AMRFinderPlus may not be relevant for clinical management or antimicrobial surveillance. See the Note regarding Genotype vs. Phenotype for more information.

===== Information =====

  * Version: 4.0.22
  * Added: May, 2025
  * Link: https://github.com/ncbi/amr

===== Usage =====

See versions which are available:
<code>$ module avail amrfinder</code>

Load one version into your environment and run it:
<code>$ module load amrfinder/4.0.22</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /var/scratch
$ git clone --recurse-submodules https://github.com/ncbi/amr.git -b amrfinder_v4.0.22
$ cd amr
$ make DEFAULT_DB_DIR=/export/apps/amrfinder/4.0.22/data
$ sudo mkdir -p /export/apps/amrfinder/4.0.22 /export/apps/amrfinder/4.0.22/data
$ sudo chown aorth /export/apps/amrfinder/4.0.22 /export/apps/amrfinder/4.0.22/data
$ make install INSTALL_DIR=/export/apps/amrfinder/4.0.22
$ module load blast/2.12.0+ hmmer/3.3
$ /export/apps/amrfinder/4.0.22/amrfinder -U
$ sudo chown -R root:root /export/apps/amrfinder/4.0.22</code>