3D De Bruijn Genome Assembly Graph

Short-read genome assemblers rarely compare reads to each other directly — instead they slice every read into overlapping k-mers and let those k-mers build a single graph, where reconstructing the genome means walking every edge of that graph exactly once. This simulator builds that de Bruijn graph in 3D from a randomly generated model genome: nodes are the distinct (k−1)-length sequence fragments observed across all reads, edges are the k-mers connecting them, and a force-directed layout lets the graph settle into its own shape live. A traversal pulse then walks the assembler's best path through it, while k-mer size, coverage and sequencing error rate control how connected — or how fractured by dead-end tips and repeat bubbles — that graph turns out to be.