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Next-Generation DNA Sequencing Informatics


Subject Area(s):  Genetics and Genome ScienceMolecular BiologyBioinformatics

Edited by Stuart M. Brown, New York University School of Medicine
   

© 2013 • 241 pp., illus. (48 4C & 15 B&W), index
Hardcover • $59 • ISBN  978-1-936113-87-3


Description

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.

Please see the Table of Contents below to purchase individual chapters.

 

Reviews

review:  “Here researchers at New York University’s Langone Medical Center provide an overview of many core types of next-generation sequencing projects, discuss methods embodied in popular software, and describe in detail their own best practice workflows. The information and advice could help both bioinformaticians implementing their own data and analysis method, and laboratories and clinical investigators planning to use next-generation sequencing methods for research.”
      —Book News Inc.

 
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Contents

Click on the chapter title to purchase individual chapters as PDFs.
 
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
 
 
          
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