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Installing AMRFinder
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.
We provide instructions for three methods of installation. The simplest, and recommended method is to install AMRFinderPlus and all of the prerequisites with bioconda. See Install with bioconda.
You will need to have the prerequisites BLAST+, HMMER, and libcurl installed. See Bioconda prerequisite installation for instructions to install them with bioconda.
If you have the prerequisites installed we have the following installation instructions. See below for instructions on installing the prerequisites with bioconda.:
- New in AMRFinderPlus
- Documentation for AMRFinder v1 (Depricated)
- Overview
- Install with bioconda (recommended)
- Docker Image
- Install with binary
- Compile from source
- Test your installation
- Usage (syntax/options)
- --organism option
- Examples
- Input file formats
- Output format
- Common errors
- Known issues
- Tips and tricks
- Database updates
- Software upgrades
- Genotypes vs. Phenotypes
- Scope: plus vs. core
- AMRFinderPlus "Method" column
- Element type and Subtype
- Class and Subclass