Design and Simulation of Hybrid de novo DNA Sequence Assembly for Large Eukaryotic Genomes

Abstract

We propose an approach for de novo DNA sequence assembly using very short reads of a large eukaryotic genome. Our assembler combines two main approaches in DNA sequence assembly, Overlap Layout Consensus (OLC) and Eulerian Path, with two types of reads to obtain significant contigs. This approach will be applied in a parallel environment. In this paper, we presentthe data and functional requirements for implementation in our assembler. We also present our hybrid assembler strategy and architecture. We simulate the core of thehybrid assembly and find that the hybrid strategy tends to produce long contigs. It is expected that this approach will generate an accurate and efficient DNA sequence assembly for large eukaryotic genomes.