Preface Acknowledgments About the Authors 1 Introduction to DNA Sequencing Stuart M. Brown 2 Quality Control and Data Preprocessing Stuart M. Brown 3 History of Sequencing Informatics Stuart M. Brown 4 Public Sequence Databases Stuart M. Brown 5 Visualization of Next-Generation Sequencing Data Phillip Ross Smith, Kranti Konganti, and Stuart M. Brown 6 DNA Sequence Alignment Efstratios Efstathiadis 7 Genome Assembly Using Generalized de Bruijn Digraphs D. Frank Hsu 8 De Novo Assembly of Bacterial Genomes from Short Sequence Reads Silvia Argimón and Stuart M. Brown 9 De Novo Transcriptome Assembly Lisa Cohen, Steven Shen, and Efstratios Efstathiadis 10 Genome Annotation Steven Shen and Stuart M. Brown 11 Using Next-Generation Sequencing to Detect Sequence Variants Jinhua Wang, Zuojian Tang, and Stuart M. Brown 12 ChIP-seq Stuart M. Brown, Zuojian Tang, Christina Schweikert, and D. Frank Hsu 13 RNA Sequencing with Next-Generation Sequencing Stuart M. Brown and Jeremy Goecks 14 Metagenomics Guillermo I. Perez-Perez, Miroslav Blumenberg, and Alexander V. Alekseyenko 15 Proteogenomics Kelly V. Ruggles and David Fenyö 16 Emerging DNA Sequencing Technologies and Applications Gerald A. Higgins and Brian D. Athey 17 Cloud-Based Next-Generation Sequencing Informatics Konstantinos Krampis, Efstratios Efstathiadis, and Stuart M. Brown Glossary Index

Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making genome and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene expression, transcription factor analysis, metagenomics, and epigenetics. Bioinformatics methods to support DNA sequencing have become and remain a critical bottleneck for many researchers and organizations wishing to make use of NGS technology. This new edition provides a thorough, plain-language introduction to the necessary informatics methods and tools for analyzing NGS data and provides detailed descriptions of algorithms, strengths and weaknesses of specific tools, pitfalls, and alternative methods. Four new chapters cover experimental design, sample preparation, and quality assessment of NGS data; public databases for DNA sequencing data; de novo transcript assembly; proteogenomics; and emerging sequencing technologies. The remaining chapters from the first edition have been updated with the latest information. This book also provides extensive reference to best-practice bioinformatics methods for NGS applications and tutorials for common workflows. This edition addresses the informatics needs of students, laboratory scientists, and computing specialists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies.