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Next-generation DNA sequencing (NGS) technology has revolutionized biomedical research, making complete genome sequencing an affordable and frequently used tool for a wide variety of research applications. Bioinformatics methods to support DNA sequencing have become a critical bottleneck for many researchers and organizations wishing to make use of NGS technology. This book provides a thorough introduction to the necessary informatics methods and tools for operating NGS instruments and analyzing NGS data. The book also provides extensive reference to best-practice bioinformatic methods for the most commonly used NGS technologies and applications. The book also includes reference to, and guidance on, the setup and use of essential software for NGS data analysis. This is the first book of its kind to address the informatics needs of scientists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies.

 

Contents

 

Preface

Acknowledgments

About the Authors

1. Introduction to DNA Sequencing

Stuart M. Brown

2. History of Sequencing Informatics

3. Visualization of Next-Generation Sequencing Data

Phillip Ross Smith, Kranti Konganti, and Stuart M. Brown

4. DNA Sequence Alignment

Efstratios Efstathiadis

5. Genome Assembly Using Generalized de Bruijn Digraphs

D. Frank Hsu

6. De Novo Assembly of Bacterial Genomes from Short Sequence Reads

Silvia Argimón and Stuart M. Brown

7. Genome Annotation

Steven Shen

8. Using NGS to Detect Sequence Variants

Jinhua Wang, Zuojian Tang, and Stuart M. Brown

9. ChIP-seq

Zuojian Tang, Christina Schweikert, D. Frank Hsu, and Stuart M. Brown

10. RNA Sequencing with NGS

Stuart M. Brown, Jeremy Goecks, and James Taylor

11. Metagenomics

Alexander Alekseyenko and Stuart M. Brown

12 High-Performance Computing in DNA Sequencing Informatics

Efstratios Efstathiadis and Eric R. Peskin

Glossary

Index