Chapter 1 Introduction

Chapter 3 Applications of High-Throughput Sequencing

Chapter 4 Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing

Chapter 5 Base-Calling for Bioinformaticians

Chapter 6 De Novo Short-Read Assembly

Chapter 7 Short-Read Mapping

Chapter 8 DNA–Protein Interaction Analysis (ChIP-Seq)

Chapter 9 Generation and Analysis of Genome-Wide DNA Methylation Maps

Chapter 10 Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

Chapter 11 MicroRNA Expression Profiling and Discovery

Chapter 12 Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data

Chapter 13 Analysis of Metagenomics Data

Chapter 14 High-Throughput Sequencing Data Analysis Software: Current State and Future Developments