Genomic String Reconstruction with Paired De Bruijn Graphs

Genome sequencing generates millions of short, paired reads that must be stitched back together to decode an organism's DNA. Understanding how to reconstruct these genomic strings is a fundamental skill in modern bioinformatics and computational biology. This text-based course guides you through the core mathematical and algorithmic concepts used to solve the sequence assembly problem. You will learn how to represent genomic data as paired de Bruijn graphs and apply classic graph-traversal algorithms to reconstruct the original sequence. What you'll learn: - Understand the foundational concepts of DNA sequencing, k-mers, and paired-end reads. - Construct paired de Bruijn graphs from gapped patterns and paired reads. - Apply Eulerian path algorithms to traverse complex genomic graphs systematically. - Reconstruct genomic strings using the string spelled by gapped patterns algorithm. - Implement these bioinformatics algorithms in clean, modern Python using structured data types. - Analyze common sequence assembly challenges, including genomic repeats and structural variations. Starting with basic terminology and foundational definitions of graph theory, this course walks you step-by-step through graph construction, path-finding algorithms, and final sequence reconstruction. It is designed for beginners in bioinformatics, computer science students, or programmers curious about genomic algorithms, requiring only basic programming knowledge. Start reading today to master the algorithmic core of modern genome assembly.