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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.

Download a Free Excerpt from Next-Generation DNA Sequencing Informatics, Second Edition:

Preface and Contents
Chapter 13: RNA Sequencing with Next-Generation Sequencing
Index

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Description
Contents
   

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


 

Description

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.

 
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Contents

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
 

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Next-Generation DNA Sequencing Informatics, Second Edition