q2-amr

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

Installation

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

macOS (intel) / Linux

mamba create -yn q2-amr \
  -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-amr

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

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

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.