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Next-generation DNA Sequencing Informatics
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, metageno...
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| Format: | Printed Book |
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Cold Spring Harbor Laboratory Press
2015
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| Edition: | 2nd |
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Table of 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