Resfinder & CARD Database Integration Tool

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:

• Resfinder
• CARD
• Python 3.8 or higher

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