Supregraph: Enabling Information-Optimal Assembly Graph Representation of a Read Set

arXiv:2604.21951v1 Announce Type: new
Abstract: The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs. However, both standard approaches are known to have limitations. De Bruijn graphs fail to represent complete information from reads, while the overlap graphs often produce artificial breaks in contigs due to the necessity to discard contained reads as a preliminary step. In this work we present a mathematical model for genome assembly that provides a formal framework to determine what constitutes a correct conversion of a read set into an assembly graph under the assumption of error-free reads. We prove that a correct representation of a read set exists in the form of a new class of assembly graphs, which we call supregraphs. We show that supregraphs can be constructed by iteratively transforming de Bruijn graphs using the multiplexing procedure, previously employed in the genome assemblers LJA and Verkko. Finally, we demonstrate that, under a set of natural assumptions, supregraphs provide a foundation for constructing theoretically optimal genome assemblies.