Next-Generation DNA Sequencing Informatics

About this book

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.

Next-Generation DNA Sequencing Informatics, Second edition, provides thorough, plain language introduction to the necessary informatics methods and tools for analyzing NGS data as did the first edition, and provides detailed descriptions of algorithms, strengths and weaknesses of specific tools, pitfalls and alternative methods. Four new chapters in this edition 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.

Next-Generation DNA Sequencing Informatics also provides extensive reference to best-practice bioinformatics methods for NGS applications and tutorials for common workflows. The second edition of Next-Generation DNA Sequencing Informatics 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.

Contents

(preliminary)
1) Introduction to DNA Sequencing
    Stuart Brown
2) Experimental Design, Sample Preparation, and Quality Assessment of NGS Data
    Adriana Heguy and Stuart Brown
3) History of Sequencing Informatics
    Stuart Brown
4) Public Databases for DNA Sequencing Data
    Stuart Brown and Philip Ross Smith
5) Visualization of NGS Data
    Philip Ross Smith, Kranti Konganti, and Stuart Brown
6) DNA Sequence Alignment
    Efstratios Efstathiadis
7) Genome Assembly Using de Bruijin Digraphs
    Frank Hsu
8) De novo Assembly of Bacterial Genomes
    Silvia Argimon
9) De novo Transcriptome Assembly
    Lisa Cohen
10) Genome Annotation
    Steven Shen and Stuart Brown
11) Using NGS to Detect Genome Sequence Variants
    Jinhua Wang
12) ChIP-seq
    Stuart Brown, Zuojian Tang, Christina Schweikert, and Frank Hsu
13) RNA-seq
    Stuart Brown and Jeremy Goecks
14) Metagenomics
    Alexander Alekseyenko, Laura Cox, and Guillermo Perez-Perez
15) Proteogenomics
    Kelly Ruggles and David Fenyo
16) Emerging DNA Sequencing Technologies
    Gerry Higgins and Brian D. Athey
17) High Performance Computing and Cloud-based NGS Informatics
    Efstratios Efstathiadis, Ross Smith, and Ntino Krampis
Index

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