Installing AMRFinder

Installation

AMRFinderPlus requires HMMER, BLAST+, Linux, and perl. We provide Linux binaries, and the source code is available to compile AMRFinderPlus yourself though we haven't extensively tested compiling AMRFinderPlus on other systems and aren't supporting non-Linux systems at this time.

For basic instructions on compiling AMRFinderPlus see Compile AMRFinderPlus from source.

Prerequisites

We recommend using Bioconda to install the prerequisites and provide instructions for how to do that below, however that's just a suggestion. You may already have all of the prerequisites installed in another way. Notably you will need libcurl and the executables for BLAST and HMMER will need to be in your path. Note, it's not a prerequisite, but these instructions use Borne shell syntax (e.g., bash). If you're using another shell you might have to modify them slightly.

Bioconda

While not strictly a prerequisite Bioconda is how we recommend installing the prerequisites. If you don''t have bioconda already installed you should run the following

~$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
~$ bash ./Miniconda3-latest-Linux-x86_64.sh # Follow prompts to accept license, choose install path, and allow the new bin directory to be added to .bashrc
~$ export PATH=$HOME/miniconda3/bin:$PATH # Change to match installation location, if not default.
~$ conda config --add channels defaults
~$ conda config --add channels bioconda
~$ conda config --add channels conda-forge

Install the prerequisites

With bioconda the three prerequisites can be installed in one command

~$ conda install -y blast hmmer libcurl

Installing AMRFinderPlus itself

~$ mkdir amrfinder && cd amrfinder
~/amrfinder$ curl -sL https://ftp.ncbi.nlm.nih.gov/pathogen/Technical/AMRFinder_technical/amrfinder_binaries_v3.0-alpha.3.tar.gz | tar xvz
~/amrfinder$ ./amrfinder -u
~/amrfinder$ ./amrfinder -p test_prot.fa

Note that to run AMRFinderPlus you will need to have the BLAST and HMMER binaries in your path. If you installed the prerequisites with bioconda as recommended above you may need to run the following, log out, and log back in before AMRFinderPlus will work.

~/miniconda3/bin/conda init

Test your installation

./amrfinder -p test_prot.fa -g test_prot.gff > test_prot.got
diff test_prot.expected test_prot.got

There should be no differences in output

Email

If you are still having trouble installing AMRFinderPlus or have any questions let me know by emailing us at [email protected].

NOTE: The handling of threading is incomplete, this version will not run on machines with < 4 cores.

Usage:

# print a list of command-line options
amrfinder --help 

# Download the latest AMRFinderPlus database
amrfinder -u

# Protein AMRFinderPlus
amrfinder -p <protein.fa> 

# Translated nucleotide AMRFinderPlus genes
amrfinder -n <assembly.fa>

# protein AMRFinderPlus using GFF to get genomic coordinates
amrfinder -p <protein.fa> -g <protein.gff> 

# search for AMRFinderPlus genes and Campylobacter protein mutations
amrfinder -p <protein.fa> -O Campylobacter 

# Search for everything AMRFinderPlus can find:
# AMR genes, plus genes, protein and nucleotide point mutations and combine results
amrfinder -p <protein.fa> -O Campylobacter -g <protein.gff> -n <assembly.fa> 

The one fragile part of running combined nucleotide and protein analyses is the association between proteins and GFF file lines. AMRFinderPlus works with NCBI's public formats for those files, but since there's no standard for how to associate FASTA entries with GFF lines it can be finicky. If you have any problems email us at [email protected] with examples.