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 in the QIIME2 library.

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 in the QIIME2 library.

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 in the QIIME2 library.

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 in the QIIME2 library.

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.