An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis

Abstract The dramatic fall in the cost of DNA sequencing has revolutionized the experiments within reach in the life sciences. Here we provide an introduction for the domains of analyses possible using high-throughput sequencing, distinguishing between "counting" and "reading" applications. We discuss the steps in designing a high-throughput sequencing experiment, introduce the most widely used applications, and describe basic sequencing concepts. We review the various software programs available for many of the bioinformatics analysis required to make sense of the sequencing data. We hope that this introduction will be accessible to biologists with no previous background in bioinformatics, yet with a keen interest in applying the power of high-throughput sequencing in their research.