Next-generation sequencing (NGS) is providing the ability to sequence genomes at an unprecedented rate and has been driving a new understanding and application of genetics in both human disease and general biology. The applications of this technology range from Mendelian gene discovery, cancer, genome assembly and de novo sequencing, to gene expression and functional genomic studies. In recent years, NGS has been increasingly applied to clinical translational research and diagnostics where it is helping to improve our ability to diagnose genetic disorders and to stratify cancer patients for therapy based on the somatic mutations in their tumours. Underlying these enormous advances in the application of this technology are the successful generation and bioinformatic processing of the resulting short read data. This talk will give a brief overview of the steps involved in an NGS experiment and will provide the foundation for the talks and exercises that follow later in the day. The talk will briefly introduce template enrichment, library preparation, sequencing, and read alignment and then discuss common strategies for variant calling from short read data.