Comparative View of In Silico DNA Sequencing Analysis Tools

DNA sequencing is an important tool for discovery of genetic variants. The task of detecting single-nucleotide variants is complicated by noise and sequencing artifacts in sequencing data. Several in silico tools have been developed to assist this process. These tools interpret the raw chromatogram data and perform a specialized base-calling and quality-control assessment procedure to identify variants. The approach used to identify variants differs between the tools, with some specific to SNPs and other for Indels. The choice of a tool is guided by the design of the sequencing project and the nature of the variant to be discovered. In this chapter, these tools are compared to facilitate the choice of a tool used for variant discovery.