ABSTRACT
This chapter presents an outline of the basic wet lab procedures to prepare the sample’s DNA for whole-genome sequencing (WGS). It follows an overview and benefits of the available sequencing technologies, and basics of WGS workflows, pipeline scripting standards and languages, and state-of-the-art workflow editors. This chapter explains the steps involved in a typical WGS workflow for short germline variant discovery, describing the algorithms, tools, file formats, and databases necessary to sustain the WGS workflows in the primary, secondary and tertiary analysis stages. It also outlines some large-scale WGS projects and applications in population genomics, disease-oriented studies, use of low-coverage WGS, and clinical uses. A summary of the challenges faced by WGS bioinformatics is also covered.
