Metadata-Version: 2.4
Name: q2-amrfinderplus
Version: 2026.7.0.dev0
Summary: A plugin to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences with NCBI-AMRFinderPlus.
Author-email: Vinzent Risch <risch.vinzent@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2024, Laboratory of Food Systems Biotechnology
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://github.com/bokulich-lab/q2-amrfinderplus
Project-URL: Repository, https://github.com/bokulich-lab/q2-amrfinderplus
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: license-file

# 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://library.qiime2.org/quickstart/pathogenome)
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 used is
[AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/).
For details on the package, please refer to the
[AMRFinderPlus documentation](https://github.com/ncbi/amr/wiki)).
Checkout the [MOSHPIT docs](https://moshpit.qiime2.org/en/stable/chapters/tutorials/amr-gene-annotation/q2-amrfinderplus/intro/)
for a tutorial of _q2-amrfinderplus_.

| Action                 | Description                                                                                 |
|------------------------|---------------------------------------------------------------------------------------------|
| fetch-amrfinderplus-db | Download AMRFinderPlus database.                                                            |
| annotate               | Annotate protein sequences, MAGs or contigs with antimicrobial resistance gene information. |
| create-feature-table   | Create a gene per contig frequency table from annotations.                                  |

## 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.
