1. An Introduction to High-throughput Sequencing Experiments: Design and Bioinformatics Analysis Rachelly Normand and Itai Yanai 2. Compressing Resequencing Data with GReEn Armando J. Pinho Diogo Pratas Sara P. Garcia 3. On the Accuracy of Short Read Mapping Peter Menzel , Jes Frellsen , Mireya Plass, Simon H. Rasmussen, and Anders Krogh 4. Statistical Modeling of Coverage in High-Throughput Data David Golan and Saharon Rosset 5. Assembly Algorithms for Deep Sequencing Data: Basics and Pitfalls Nitzan Kol and Noam Shomron 6. Short Reads Mapping for Exome Sequencing Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, and You-Qiang Song 7. -Profiling Short Tandem Repeats from Short Reads Melissa Gymrek and Yaniv Erlich 8. Exome Sequencing Analysis: A Guide to Disease Variant Detection Ofer Isakov, Marie Perrone, and Noam Shomron 9. Identifying RNA Editing Sites in miRNAs by Deep Sequencing Shahar Alon and Eli Eisenberg 10. Identifying Differential Alternative Splicing Events from RNA Sequencing Data using RNASeq-MATS Juw Won Park, Collin Tokheim, Shihao Shen, and Yi Xing 11. Optimizing Detection of Transcription Factor Binding Sites in ChIP-seq Experiments Aleksi Kallio and Laura L. Elo 12. Statistical Analysis of ChIP-seq Data with MOSAiCS Guannan Sun, Dongjun Chung, Kun Liang, and Sunduz Keles 13. Detection of Reverse Transcriptase Termination Sites using cDNA Ligation and Massive Parallel Sequencing Lukasz J. Kielpinski, Mette Boyd, Albin Sandelin, and Jeppe Vinther