Partial DNA Assembly: A Rate-Distortion Perspective

TL;DR

This paper introduces a rate-distortion framework for partial DNA assembly, defining a new distortion measure based on the number of Eulerian cycles in assembly graphs, and presents an algorithm with real genome analysis.

Contribution

It proposes a novel distortion function for assembly graphs and develops an algorithm for partial DNA assembly under this framework.

Findings

The distortion measure is the logarithm of Eulerian cycles in the assembly graph.

The algorithm effectively constructs assembly graphs from real genome data.

The approach provides a new perspective on handling ambiguous DNA assemblies.

Abstract

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the assembly graph, each of which correspond to a candidate assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an assembly graph and analyze its performance on real genomes.