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Welcome to the q2-amrfinderplus wiki!

Installation

Please refer to the installation instructions for Qiime2.

Usage Tutorial

This tutorial will show you how to annotate assembled sequences with antimicrobial resistance genes (ARGs) using the q2-amrfinderplus plugin. The functionalities of the plugin include:

• Download the AMRFinderPlus database with the fetch-amrfinderplus-db action.
• Annotate assembled sequences using the annotate action.

Download the database

To download the AMRFinderPlus database you can use the fetch-amrfinderplus-db action. It automatically downloads the newest version of the database.

qiime amrfinderplus fetch-amrfinderplus-database \
  --output-dir amrfinderplus_database

Test data

test_data_q2_amrfinerplus.zip

Annotate

To annotate assembled sequences with ARGs you can use the annotate action. The action can take sequences (SampleData[MAGs], SampleData[Contigs] and FeatureData[MAG]), proteins (GenomeData[Proteins]) and loci (GenomeData[Loci]) as inputs. Predicted proteins and loci can be created from MAGs with the action predict-prodigal from q2-moshpit. For information on the parameters please run qiime amrfinderplus annotate --help and consult the AMRFinderPlus documentations. It is recommended to run annotate in the combined mode with predicted proteins and loci, as this is the most sensitive. However it is possible to run annotate with only sequences or with only proteins.

qiime amrfinderplus annotate \
  --i-amrfinderplus-db amrfinderplus-db.qza \
  --i-sequences mags.qza \
  --i-proteins proteins.qza \
  --i-loci loci.qza \
  --p-organism Escherichia \
  --output-dir amr_annotations

Tabulate ARG annotations

With the tabulate visualizer of the q2-metadata plugin it is possible to generate a tabular view of ARG annotations. The output visualization supports interactive filtering, sorting, and exporting to common file formats.
First you have to install q2-metadata into your environment.

mamba install \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.10/metagenome/released/ \
  q2-metadata

Run visualizer:

qiime metadata tabulate \
  --m-input-file annotations.qza \
  --o-visualization annotations_tabulated.qzv

qiime metadata tabulate \
  --m-input-file mutations.qza \
  --o-visualization annotations_tabulated.qzv