Next-generation sequencing (NGS) technologies have rapidly evolved in the last 5 years, leading to the generation of millions of short reads in a single run. Consequently, various sequence alignment algorithms have been developed to compare these reads to an appropriate reference in order to perform important downstream analysis. SOAP2 from the SOAP series is one of the most commonly used alignment programs to handle NGS data, and it efficiently does so using low computer memory usage and fast alignment speed. This chapter describes the protocol used to align short reads to a reference genome using SOAP2, and highlights the significance of using the in-built command-line options to tune the behavior of the algorithm according to the inputs and the desired results.
Keywords: Burrows–Wheeler transform (BWT ); Gapped alignment; Genome index ing; Genomics; Match mode; Mismatches; Next-generation sequencing; Nucleotides; Read map ping; Repeats; SNP prediction; Seed length; Short read alignment; Structural variant; Ungapped alignment.