QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.
To install q2-rgi, follow the steps described in the QIIME2 library.
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.
| Action | Description | Underlying tool | Used function |
|---|---|---|---|
| fetch-card-db | Download and preprocess CARD and WildCARD data. | rgi | card_annotation, wildcard_annotation |
| annotate-mags-card | Annotate MAGs with antimicrobial resistance gene information from CARD. | rgi | main, load |
| annotate-reads-card | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | rgi | bwt, load |
| heatmap | Create a heatmap from annotate-mags-card output files. | rgi | heatmap |
| kmer-query-mags-card | Pathogen-of-origin prediction for ARGs in MAGs. | rgi | kmer-query, load |
| kmer-query-reads-card | Pathogen-of-origin prediction for ARGs in reads. | rgi | kmer-query, load |
| kmer-build-card | Build a kmer database with a custom kmer length. | rgi | kmer-build |
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.