q2-rgi

bokulich-lab

CI codecov Code style: black

QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.

Installation

To install q2-rgi, follow the steps described below.

macOS (intel) / Linux
mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info
macOS (apple silicon)
CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info

Functionality

This QIIME 2 plugin contains actions used to annotate short single/paired-end sequencing reads and MAGs with antimicrobial resistance genes. Currently, the CARD database is supported (for details on the implementation and usage, please refer to the rgi documentation). Below you will find an overview of actions available in the plugin.

ActionDescriptionUnderlying toolUsed function
fetch-card-dbDownload and preprocess CARD and WildCARD data.rgicard_annotation, wildcard_annotation
annotate-mags-cardAnnotate MAGs with antimicrobial resistance gene information from CARD.rgimain, load
annotate-reads-cardAnnotate metagenomic reads with antimicrobial resistance gene information from CARD.rgibwt, load
heatmapCreate a heatmap from annotate-mags-card output files.rgiheatmap
kmer-query-mags-cardPathogen-of-origin prediction for ARGs in MAGs.rgikmer-query, load
kmer-query-reads-cardPathogen-of-origin prediction for ARGs in reads.rgikmer-query, load
kmer-build-cardBuild a kmer database with a custom kmer length.rgikmer-build

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.

CI codecov Code style: black

QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.

Installation

To install q2-rgi, follow the steps described below.

macOS (intel) / Linux
mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info
macOS (apple silicon)
CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info

Functionality

This QIIME 2 plugin contains actions used to annotate short single/paired-end sequencing reads and MAGs with antimicrobial resistance genes. Currently, the CARD database is supported (for details on the implementation and usage, please refer to the rgi documentation). Below you will find an overview of actions available in the plugin.

ActionDescriptionUnderlying toolUsed function
fetch-card-dbDownload and preprocess CARD and WildCARD data.rgicard_annotation, wildcard_annotation
annotate-mags-cardAnnotate MAGs with antimicrobial resistance gene information from CARD.rgimain, load
annotate-reads-cardAnnotate metagenomic reads with antimicrobial resistance gene information from CARD.rgibwt, load
heatmapCreate a heatmap from annotate-mags-card output files.rgiheatmap
kmer-query-mags-cardPathogen-of-origin prediction for ARGs in MAGs.rgikmer-query, load
kmer-query-reads-cardPathogen-of-origin prediction for ARGs in reads.rgikmer-query, load
kmer-build-cardBuild a kmer database with a custom kmer length.rgikmer-build

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.

CI codecov Code style: black

QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.

Installation

To install q2-rgi, follow the steps described below.

macOS (intel) / Linux
mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info
macOS (apple silicon)
CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info

Functionality

This QIIME 2 plugin contains actions used to annotate short single/paired-end sequencing reads and MAGs with antimicrobial resistance genes. Currently, the CARD database is supported (for details on the implementation and usage, please refer to the rgi documentation). Below you will find an overview of actions available in the plugin.

ActionDescriptionUnderlying toolUsed function
fetch-card-dbDownload and preprocess CARD and WildCARD data.rgicard_annotation, wildcard_annotation
annotate-mags-cardAnnotate MAGs with antimicrobial resistance gene information from CARD.rgimain, load
annotate-reads-cardAnnotate metagenomic reads with antimicrobial resistance gene information from CARD.rgibwt, load
heatmapCreate a heatmap from annotate-mags-card output files.rgiheatmap
kmer-query-mags-cardPathogen-of-origin prediction for ARGs in MAGs.rgikmer-query, load
kmer-query-reads-cardPathogen-of-origin prediction for ARGs in reads.rgikmer-query, load
kmer-build-cardBuild a kmer database with a custom kmer length.rgikmer-build

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.

CI codecov Code style: black

QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.

Installation

To install q2-rgi, follow the steps described below.

macOS (intel) / Linux
mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info
macOS (apple silicon)
CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm

conda activate q2-rgi
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-rgi.git

Refresh cache and check that everything worked:

qiime dev refresh-cache
qiime info

Functionality

This QIIME 2 plugin contains actions used to annotate short single/paired-end sequencing reads and MAGs with antimicrobial resistance genes. Currently, the CARD database is supported (for details on the implementation and usage, please refer to the rgi documentation). Below you will find an overview of actions available in the plugin.

ActionDescriptionUnderlying toolUsed function
fetch-card-dbDownload and preprocess CARD and WildCARD data.rgicard_annotation, wildcard_annotation
annotate-mags-cardAnnotate MAGs with antimicrobial resistance gene information from CARD.rgimain, load
annotate-reads-cardAnnotate metagenomic reads with antimicrobial resistance gene information from CARD.rgibwt, load
heatmapCreate a heatmap from annotate-mags-card output files.rgiheatmap
kmer-query-mags-cardPathogen-of-origin prediction for ARGs in MAGs.rgikmer-query, load
kmer-query-reads-cardPathogen-of-origin prediction for ARGs in reads.rgikmer-query, load
kmer-build-cardBuild a kmer database with a custom kmer length.rgikmer-build

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.