Sequencing technologies for epigenetics: From basics to applications

Recent advances in sequencing technologies, namely next-generation and third-generation sequencing, have had a major impact on biomedical research in many different fields, including epigenetics and immunological research. Although these technologies have a common goal, the experimental approaches and techniques used by the different sequencing platforms may differ significantly, leading to both specific advantages and characteristic shortcomings. To harness their full potential by selecting the appropriate technology for a biological problem at hand, and to perform an appropriate computational analysis of the generated sequencing data, it is imperative to have a basic understanding of how the technologies work and what individual strengths and weaknesses they have. This chapter provides an introductory, necessarily incomplete overview of these sequencing technologies, and the computational analysis of the data that they produce. A particular focus will lie on their application to study the epigenetic regulation of cellular functions in the context of the immune system, but most considerations hold for other research fields as well.