© 2015 • 402 pages, illustrated (81 color, 20 B&W), index
Hardcover • $55.52 • ISBN 978-1-621821-23-6

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.

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