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Single-Molecule Sequencing: Training, Methods, and Applications

Overview

Sequencing-based research has become the dominant investigative practice within the biological sciences. This repository, "Single-molecule sequencing: training, methods, and applications," provides a comprehensive, hands-on, and in-depth introduction to sequencing technologies for students. Covering techniques from Sanger to third-generation technologies, this course alternates between lectures and labs, introducing students to the fundamental principles of DNA and RNA science. It progresses through cutting-edge library preparation and sequencing analysis techniques using Illumina and Nanopore technologies. Participants will perform direct-RNA sequencing on research samples and explore the ethical implications of data handling. The course also integrates relevant concepts in biology and computer science.

Repository Structure

This repository is organized into course modules, each contained in separate folders corresponding to the course structure. Below is a description of each folder and its contents.

C1: What is Single-Molecule Sequencing

  • L1_Single-Molecule-Sequencing_Methods_Training_Applications_V3.pdf: Slide deck covering the course introduction & motivation, single-molecule fluorescence, and traditional next-generation sequencing technologies.
  • HW1_Notebook_Setup_Single_Molecule_Sequencing_Methods_Training_Applications.ipynb: Google Colab setup notebook.

C2: Dry Lab Practice & Single-Molecule Sequencing Formats

C3: Epigenomes, DNA Modifications, and Single-Molecule DNA-sequencing

C4: Wet Lab Practice & Material Collection

C5: Epitranscriptomics, RNA Modifications, and Single-Molecule RNA-sequencing

C6: Preparing a Sequencing Library

C7: Machine Learning and Systems Biology

C8: Independent Nanopore direct-RNA sequencing Analysis

C9: Single-Molecule Proteomic Sequencing & Genome Genetics-Ethics

C10: Student Poster Presentation

Getting Started

To get started with the course materials in this repository, clone the repository to your local machine using the following command:

git clone [https://github.com/Theo-Nelson/SMS-colab.git](https://github.com/Theo-Nelson/SMS-colab.git)
git