q2-amrfinderplus

bokulich-lab

Code style: 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 for the pathogenome distribution. The pathogenome distribution is only available for linux. If you want to install q2-amrfinderplus on macOS you can install it with the tiny distribution. For this follow the instructions on the QIIME2 Library.

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. For a tutorial on the package, please refer to the MOSHPIT docs

ActionDescription
fetch-amrfinderplus-dbDownload AMRFinderPlus database.
annotateAnnotate protein sequences, MAGs or contigs with antimicrobial resistance gene information.
create-feature-tableCreate 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.

Code style: 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 for the pathogenome distribution. The pathogenome distribution is only available for linux. If you want to install q2-amrfinderplus on macOS you can install it with the tiny distribution. For this follow the instructions on the QIIME2 Library.

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. For a tutorial on the package, please refer to the MOSHPIT docs

ActionDescription
fetch-amrfinderplus-dbDownload AMRFinderPlus database.
annotateAnnotate protein sequences, MAGs or contigs with antimicrobial resistance gene information.
create-feature-tableCreate 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.

Code style: 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 for the pathogenome distribution. The pathogenome distribution is only available for linux. If you want to install q2-amrfinderplus on macOS you can install it with the tiny distribution. For this follow the instructions on the QIIME2 Library.

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. For a tutorial on the package, please refer to the MOSHPIT docs

ActionDescription
fetch-amrfinderplus-dbDownload AMRFinderPlus database.
annotateAnnotate protein sequences, MAGs or contigs with antimicrobial resistance gene information.
create-feature-tableCreate 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.

Code style: 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 for the pathogenome distribution. The pathogenome distribution is only available for linux. If you want to install q2-amrfinderplus on macOS you can install it with the tiny distribution. For this follow the instructions on the QIIME2 Library.

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. For a tutorial on the package, please refer to the MOSHPIT docs

ActionDescription
fetch-amrfinderplus-dbDownload AMRFinderPlus database.
annotateAnnotate protein sequences, MAGs or contigs with antimicrobial resistance gene information.
create-feature-tableCreate 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.