AMRNanoPro: An Antimicrobial Resistance Analysis Pipeline for Nanopore Sequencing Data

Introduction

AMRNanoPro is a Nextflow pipeline designed to analyze Nanopore sequencing data for antimicrobial resistance (AMR) detection in bacteria isolates whole genome sequencing data. It integrates quality control, filtering, and comprehensive reporting tools to facilitate rapid and accurate AMR profiling. The next steps are to add Flye for assembly, medaka for polishing and Abricate for AMR profiling. At the end, the input processing will support directory and sample sheet for batch processing. This pipeline is ideal for researchers and clinicians who need a streamlined and reproducible workflow for processing Nanopore sequencing data in the context of antimicrobial resistance studies.

Links

• GitHub Repository: AMRNanoPro
• Project Blog Article: AMRNanoPro: A Nextflow Pipeline for Comprehensive Bacterial Genome Analysis from Quality Control to Antimicrobial Resistance Profiling
• Author LinkedIn:
  • Albert Rock A. Gangbadja

Installation

Prerequisites

• Nextflow version 23.04.4 or higher
• Java version 11 or higher
• Docker

Steps

1. Install Dependencies:

   • Using Docker:

     Ensure Docker is installed and running on your system.

2. Download Test Data (Optional):

   wget -O test_data.fastq.gz 

Usage

To run the pipeline with your data:

nextflow run AlbertRockG/amrnanopro \
            --input_fastq path/to/your_data.fastq.gz \
            --outdir path/to/your_output_dir \
            -profile docker

Parameters

• --input_fastq: Path to the input FASTQ file(s).
• --skip_chopper: Set to false to skip the Chopper filtering step.

Profiles

• standard: Default execution profile.
• docker: Executes processes within Docker containers.

Output

Results will be generated in the results/ directory, including:

• Quality Control Reports:
  • Pre- and post-filtering NanoPlot reports.
• Filtered Reads:
  • FASTQ files after Chopper filtering.
• MultiQC Report:
  • An aggregated report combining all quality metrics.

Contributing

We welcome contributions to improve AMRNanoPro! Please follow these steps:

1. Fork the repository on GitHub.

2. Create a new branch for your feature or bug fix:

   git checkout -b feature/your-feature-name

3. Make your changes and commit them with clear messages.

4. Push to your branch:

   git push origin feature/your-feature-name

5. Create a pull request on GitHub, describing your changes.

Code of Conduct

Please read our Code of Conduct before contributing.

Related Projects

• Nextflow
• NanoPlot
• Chopper
• MultiQC

License

This project is licensed under the MIT License - see the LICENSE file for details.

Resources

• What Your Code Repository Says About You: Read Article
• Awesome README List: GitHub Repository
• Nextflow Documentation: Nextflow Docs
• Best Practices for Writing README Files: Guide

Screenshots

MultiQC Report Overview

Figure 1: MultiQC report summarizing quality control metrics.

Thank you for using AMRNanoPro! If you have any questions or encounter issues, please open an issue on GitHub.