Page Contents

Overview

AMRFinderPlus identifies acquired antimicrobial resistance (AMR) genes, virulence genes, and stress genes. Such AMR genes confer resistance to antibiotics, metals, biocides, heat, or acid. For some taxa (see here), AMRFinderPlus will provide taxa-specific results including filtering out genes that are almost ubiquitous in the taxa (intrinsic genes) and identifying resistance-associated point mutations. In TheiaProk, the taxon used by AMRFinderPlus is specified based on the gambit_predicted_taxon or a user-provided expected_taxon.

You can check if a gene or point mutation is in the AMRFinderPlus database here, find the sequences of reference genes here, and search the query Hidden Markov Models (HMMs) used by AMRFinderPlus to identify AMR genes and some stress and virulence proteins (here). The AMRFinderPlus database is updated frequently. You can ensure you are using the most up-to-date version by specifying the docker image as a workflow input. You might like to save this docker image as a workspace data element to make this easier.

📋 Use Cases:

To run ONLY AMRFinderPlus software instead of running the entire TheiaProk workflow. This workflow will run much faster than the TheiaProk workflows.
To update AMRFinderPlus results when a new version of the software and/or its database are released by the NCBI developers.

Inputs

Input all String values (other than when selecting dropdown option Strings) in quotations, e.g. “5m”

Overview

📋 Use Cases:

Inputs

Required Inputs

Optional Inputs

Outputs

Terra Outputs

References