Genome Assembly with de Bruijn Graphs and Eulerian Paths

Reconstructing an entire genome from billions of short DNA fragments is one of the most significant computational challenges in modern science. Understanding the core graph theory algorithms behind this process is essential for anyone entering the field of bioinformatics. This text-only course guides you through the foundational concepts of genome assembly, showing you how to represent DNA reads as k-mers, construct de Bruijn graphs, and find Eulerian paths to reconstruct original sequences. You will gain a clear, conceptual and algorithmic understanding of how modern assemblers solve sequence reconstruction. What you'll learn: - Understand the basic biology of DNA sequencing reads and the computational need for assembly. - Break down DNA sequences into k-mers and construct overlap and de Bruijn graphs. - Define Eulerian paths and Eulerian circuits and understand their mathematical properties. - Apply Hierholzer's algorithm to find paths through complex genomic networks. - Analyze how modern assembly tools handle real-world sequencing errors and bubbles in graphs. - Read and trace step-by-step algorithmic pseudocode for graph traversal and sequence reconstruction. The course starts with essential terminology and the biological context of sequencing data. You will then progress from basic k-mer generation to constructing de Bruijn graphs and implementing Eulerian path algorithms through structured written explanations and walkthroughs. Designed for beginners in bioinformatics, computer science students, or biology enthusiasts, this course requires no prior background in advanced graph theory or genetics. Start reading today to master the algorithmic foundation of modern genome assembly.