QIIME 2 plugin to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences with AMRFinderPlus.
To install q2-amrfinderplus, follow the steps described in the QIIME 2 installation instructions for the pathogenome distribution .
This QIIME 2 plugin contains actions used to annotate protein sequences MAGs and contigs with antimicrobial resistance genes. The underlying tool used is AMRFinderPlus, for details on the package, please refer to the AMRFinderPlus documentation). Checkout the wiki for usage examples of q2-amrfinderplus.
| Action | Description |
|---|---|
| fetch-amrfinderplus-db | Download AMRFinderPlus database. |
| annotate | Annotate protein sequences, MAGs or contigs with antimicrobial resistance gene information. |
This repository follows the black code style. To make the development slightly easier
there are a couple of pre-commit hooks included here that will ensure that your changes
follow that formatting style. Before you start working on the code, please
install the hooks by executing make dev in your conda environment. From then on,
they will be run automatically every time you commit any changes.