q2-amr: A Plugin for Antibiotic Resistance Gene Analysis in Qiime2

Hello Qiime2 Community!

I'm excited to introduce q2-amr, a new Qiime2 plugin, designed to integrate Antibiotic Resistance Gene (ARG) analysis into Qiime2. This plugin leverages the Resistance Gene Identifier (RGI) and the Comprehensive Antibiotic Resistance Database (CARD) to detect ARGs in both reads and MAGs.

Features:

  • Data Fetching: Automatically fetch and preprocess all necessary CARD databases.
  • ARG Detection: Detect ARGs in reads and MAGs.
  • Heatmap Visualization: Generate heatmap visualizations from MAG annotations.

For installation and usage instructions, please refer to the Wiki.

I started the development of this plugin as part of my master's thesis in the lab of Prof. Dr. Nicholas Bokulich @Nicholas_Bokulich with the supervision and help of Dr. Michal Ziemski @misialq. Now I am continuing that work as part of the development team in the same lab.
q2-amr is still a work in progress and more functionalities (normalization, k-mer based taxanomic prediction, other ARG databases etc.) will be added in the future.

I hope q2-amr enhances your analysis workflows in Qiime2. Please feel free to share your feedback, report issues, or ask questions here or on GitHub!

Happy analyzing!

Vinzent

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