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-# q2-amrfinderplus
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+# q2-amrfinderplus
+
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+QIIME 2 plugin to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences with AMRFinderPlus.
+
+## Installation
+To install _q2-amrfinderplus_, follow the steps described in the [QIIME 2 installation instructions](https://docs.qiime2.org/2024.10/install/native/#qiime-2-pathogenome-distribution) for the pathogenome distribution .
+
+
+## Functionality
+This QIIME 2 plugin contains actions used to annotate protein sequences MAGs and contigs with antimicrobial resistance genes. The underlying tool is [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/), for details on
+the implementation and usage, please refer to the [documentation](https://github.com/ncbi/amr/wiki)).
+
+| Action                 | Description                                                                                |
+|------------------------|--------------------------------------------------------------------------------------------|
+| fetch-amrfinderplus-db | Download AMRFinderPlus database.                                                           |
+| annotate               | Annotate protein sequences, MAGs or contigs with antimicrobial resistance gene information.|
+
+## Dev environment
+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.