Next-Generation DNA Sequencing Informatics, Second Edition

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.

Authors

Alexander Alekseyenko
Silvia Argimón
Brian D. Athey
Miroslav Blumenberg
Stuart M. Brown
Lisa Cohen
Efstratios Efstathiadis
David Fenyö
Jeremy Goecks
Gerald A. Higgins
D. Frank Hsu
Kranti Konganti
Konstantinos Krampis
Guillermo I. Perez-Perez
Kelly V. Ruggles
Christina Schweikert
Steven Shen
Phillip Ross Smith
Zuojian Tang
Jinhua Wang

Stuart M. Brown is an Associate Professor at the NYU Center for Health Informatics and Bioinformatics. He leads a consulting group focused on Sequencing Informatics and teaches graduate Bioinformatics courses. His current research includes de novo sequencing/assembly/annotation of interesting genomes, RNA-seq gene expression studies, motif analysis of gene regulatory domains, and data management for integrative genomics projects. He is the author of Next-Generation DNA Sequencing Informatics (2012, 2015) and Essentials of Medical Genomics (2008). He received his PhD. in molecular biology from Cornell University in 1992 and his BS in Botany from the University of Michigan in 1983.

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