_____    ______   _____    _____     ____                                        
 |  __ \  |  ____| |  __ \  |  __ \   / __ \                                       
 | |__) | | |__    | |__) | | |__) | | |  | |    ______                            
 |  _  /  |  __|   |  ___/  |  _  /  | |  | |   |______|                           
 | | \ \  | |____  | |      | | \ \  | |__| |                                      
 |_|  \_\ |______| |_| _____|_|_ \_\  \____/     _______   _    _    ____    _   _ 
 | |  | |     /\      / ____| | |/ /     /\     |__   __| | |  | |  / __ \  | \ | |
 | |__| |    /  \    | |      | ' /     /  \       | |    | |__| | | |  | | |  \| |
 |  __  |   / /\ \   | |      |  <     / /\ \      | |    |  __  | | |  | | | . ` |
 | |  | |  / ____ \  | |____  | . \   / ____ \     | |    | |  | | | |__| | | |\  |
 |_|  |_| /_/    \_\  \_____| |_|\_\ /_/    \_\    |_|    |_|  |_|  \____/  |_| \_|
                                                                                   
                                                                                   

📑 Table of Contents

• Introduction
• Setup and Installation
• Contributors
• Contacts

🧬 Introduction

ReproHackathon RNASeq Pipeline reproduces findings from Peyrusson et al. (Nature Communications, 2020) on the transcriptomic profile of Staphylococcus aureus persisters under antibiotic stress. The study highlights how S. aureus persisters—cells that tolerate antibiotics without genetic resistance—may contribute to recurring infections.

Built with Nextflow and Docker, this pipeline employs RNA-Seq to study transcriptomic changes, identifying factors influencing antibiotic persistence and tolerance. It covers genome mapping, read counting, and differential expression analysis, capturing the complex adaptation of S. aureus under stress.

Key Features

• High Reproducibility: Leveraging Docker containers ensures easy deployment and consistent results across systems.
• Data Analysis: Includes genome mapping, read counting, and statistical analysis for identifying differentially expressed genes (DEGs).
• Modular Workflow: Nextflow's flexible design allows for easy customization and expansion of the pipeline. Prebuilt Docker images ensure rapid setup.

🔧 Setup and Installation

Requirements

• Nextflow v24.10.0+
• Docker v20.10.21+
• Hardware: 8 cores & 8 GB RAM minimum

Installation Instructions

# Clone this repository
git clone https://github.com/Kubilay-Meydan/ReproHackathon.git
cd ReproHackathon

# Install Nextflow if not already installed
curl -s https://get.nextflow.io | bash

# Ensure Docker is installed and running: https://docs.docker.com/get-docker/

# Launch the pipeline
Nextflow run main.nf

👥 Contributors

This project was developed by:

• Kubilay Meydan
• Nathan Carré
• Youna Maillié
• Emma Le Roy Pardonche

🗨️ Contacts

For questions, feel free to reach out to us through GitHub or connect on LinkedIn.

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