Real-Time Nanopore Analysis Pipeline

Project Overview

This repository develops a real-time Nanopore sequencing pipeline to advance cancer vaccine research. It integrates on-the-fly data analytics for immediate sequencing quality monitoring with comparative TCR analysis between Singleron and Nanopore technologies, aiming to pinpoint the most effective methods for immunotherapy applications.

Objectives

• Real-Time Sequencing Analysis: To develop data analytics capabilities for real-time monitoring of sequencing quality, establish data-informed sequencing endpoints, and provide a code-free analytics interface.
• Comparative Data Analysis: To compare the efficacy of Singleron and Nanopore technologies in analyzing TCR repertoires, determining the best method for immunotherapy applications.

Repository Content

• iteration_1: First setup of the real-time analysis pipeline using Jupyter Notebook for visualization and analysis, employing packages such as Pandas and NumPy. Sunsetted due to changes in direction of research and implementation.
• iteration_2: Enhancements and optimizations based on initial results, incorporating advanced analytics using R and integrating Mash for efficient sequence comparison.

Languages and Tools

• : Used for data analysis and visualization.
• Mash: Utilized for rapid sequence comparison, enhancing the comparative analysis of TCR repertoires.

Getting Started

To get a local copy up and running follow these simple steps:

1. Clone the repo

   git clone https://github.com/javianng/astar.git

2. Navigate to the notebook directory

   cd iteration_2

3. Open the Jupyter Notebook

   jupyter notebook

Contributing

Contributions are what make the open-source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

License

Distributed under the MIT License. See LICENSE for more information.

Contact

Project Link: https://github.com/javianng/astar