Methods for Assembling Reads and Producing Contigs

Determining the genome sequence of an organism is often the first step towards its molecular characterization. Once a difficult and expensive task, nowadays it is an almost routine practice in many molecular biology labs. In this chapter we discuss in depth the various methods to assemble the short sequences (called reads) obtained from a massive sequencing system, using different software and strategies, and how to perform some fundamental quality controls on the data obtained.