Genome Assembly Fundamentals: Reconstructing DNA with Overlap Graphs

Reconstructing a complete genome from millions of tiny DNA fragments is one of the most critical challenges in modern bioinformatics. This text-based course guides you through the foundational algorithms used to piece these sequences back together. You will transition from understanding basic DNA strings to designing and analyzing overlap graphs that solve the classic string reconstruction problem. By exploring the mathematical principles of graph theory, you will gain a clear, conceptual understanding of how modern genome assembly pipelines operate behind the scenes. What you'll learn: - Understand the core biological and computational concepts of k-mers, DNA reads, and string reconstruction. - Build overlap graphs by identifying prefix and suffix matches among DNA fragments. - Apply graph theory algorithms, including Hamiltonian and Eulerian paths, to solve assembly puzzles. - Analyze the differences between overlap graphs and modern De Bruijn graph approaches. - Identify common sequencing errors and learn computational strategies to resolve them. This course begins with essential terminology and the biological context of sequencing, then moves step-by-step through graph construction, path-finding algorithms, and modern assembly considerations. It is designed for beginners in bioinformatics, computer science students, or biology enthusiasts with no prior experience in graph theory or advanced programming. Start reading today to unlock the algorithmic secrets of genomic data.