Next‐Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences

This chapter first introduces the various DNA sequencing technologies, and then presents the methods for the assembly of sequences generated using various sequencing platforms. These next-generation sequencing technologies are classified into: pyrosequencing, sequencing by synthesis (Illumina), sequencing by ligation (SOLiD), semiconductor sequencing (Ion Torrent), and single-molecule real-time sequencing (PacBio, Helicos and Oxford Nanopore). Exact DE Novo Assembler (Edena) applies the overlap-layout-consensus (OLC) approach to homogeneous-length short reads from the SOLiD and Illumina platforms. During the library preparation and sequencing process, numerous sequence artifacts will negatively affect the quality of raw data for downstream analyses. Therefore, these quality issues necessitate better programs for quality control and preprocessing of all the raw data. Various tactics such as paired-end and mate-pair sequencing can be applied, which help the assembly of short sequences into contigs and scaffolds. There are mainly three categories of assemblers: greedy graph-based assemblers, OLC assemblers, and de Bruijn graph (DBG) based assemblers.