Next-Generation DNA Sequencing Informatics

About this book

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. Next-Generation DNA Sequencing Informatics provides a thorough introduction to the necessary informatics methods and tools for operating NGS instruments and analyzing NGS data. Next-Generation DNA Sequencing Informatics also provides extensive reference to best-practice bioinformatic methods for the most commonly used NGS technologies and applications. Next-Generation DNA Sequencing Informatics 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

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