De Bruijn Genome Assembly

This simulation walks through short-read genome assembly the way a real bioinformatics pipeline does: a DNA sequence is fragmented into overlapping reads, each read is decomposed into overlapping k-mers, and those k-mers become nodes in a de Bruijn graph, connected wherever one directly overlaps the next. An animated Eulerian-path walk then retraces the graph to reconstruct the original genome — and when the genome contains a repeated sub-sequence, the graph develops a branch point with more than one valid path, making reconstruction genuinely ambiguous from short reads alone. Choose a preset genome or type your own, tune the k-mer and read lengths, and watch the graph build and the assembly play out.