ABSTRACT
Reconstructing genomes through deoxyribonucleic acid (DNA) sequencing is an important problem in genomics. Some tailor-made genome assemblers are developed for reconstructing genomes from short reads. Their success led to a number of successful de novo genome assembly projects, including the reconstruction of James Watson’s genome and the panda genome. This chapter discusses different methods for de novo genome assembly. It discusses how the reads are sequenced from the genome. The chapter describes genome assembly methods for assembling short reads generated by second-generation sequencing. It covers the techniques for assembling long reads generated by third-generation sequencing. Finally, the chapter ends with criteria for evaluating the goodness of a genome assembly. The goodness of an assembly can be evaluated by the assembly completeness and the assembly accuracy. The chapter also includes exercises related to genome assembly.
