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Resfinder & CARD Database Integration Tool

License Python Version Platform

This repository hosts powerful scripts designed to predict antimicrobial resistance genes using the Resfinder and CARD (Comprehensive Antibiotic Resistance Database) databases. Tailored for high-throughput genomic data analysis, our tools are ready to handle multiple input files efficiently, making them perfect for batch processing.

Prerequisites

Before you begin, make sure you have installed:

Installation

Follow these steps to set up the tools for your use:

  1. Clone the repository: 
    git clone https://github.com/ParthDoshi97/AMR-GeneDetection-ResFinder-CARD.git
cd AMR-GeneDetection-ResFinder-CARD
  2. Visit the Resfinder and CARD GitHub pages for specific installation instructions:
    • Resfinder
    • CARD -

Configuration

  • Update the paths in the Bash Script to your input and output directories.
  • Customize the script settings as needed by modifying the command-line options detailed on the GitHub pages of Resfinder and CARD.

Usage

To run the scripts after installation, navigate to the directory and execute the run script:

./run_script.sh  # Replace `run_script.sh` with your script's filename.

References

Alcock et al. 2023. "CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database." Nucleic Acids Research, 51, D690-D699. PMID 36263822

Bortolaia V, et al. "ResFinder 4.0 for predictions of phenotypes from genotypes." Journal of Antimicrobial Chemotherapy. 2020 Aug 11. PMID: 32780112