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.
1) Introduction to DNA Sequencing
2) Experimental Design, Sample Preparation, and Quality Assessment of NGS Data
Adriana Heguy and Stuart Brown
3) History of Sequencing Informatics
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
7) Genome Assembly Using de Bruijin Digraphs
8) De novo Assembly of Bacterial Genomes
9) De novo Transcriptome Assembly
10) Genome Annotation
Steven Shen and Stuart Brown
11) Using NGS to Detect Genome Sequence Variants
Stuart Brown, Zuojian Tang, Christina Schweikert, and Frank Hsu
Stuart Brown and Jeremy Goecks
Alexander Alekseyenko, Laura Cox, and Guillermo Perez-Perez
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
"Next-Generation DNA Sequencing Informatics (2nd edition) [...] is a book to get you well and truly started in Bioinformatics [...] the chapters appear to flow well internally and cover the main aspects of the methods presented. Certainly the QC and RNA-seq chapters will point students or new bioinformaticians in the right direction [...] this book is likely to be a good one to have on your shelf."
– CoreGenomics blogspot