May 28, 2015

New 'Next-Gen Seq 2' book is at the printer

The second edition of the Next-Generation Sequencing Informatics book (that I edit) is at the printer and available for pre-order at Cold Spring Harbor Press and Amazon. We think it will ship on June 30th, maybe a bit sooner.

[James Hadfield at CoreGenomics blog has posted a review: ]

We have added new chapters on the latest sequencing technology, QC, de novo transcript assembly, proteogenomics and lots of updates and expansion in areas such as RNA-seq and ChIP-seq. It has a beautiful cover and its not too expensive.

Here is the official publication blurb:

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 Bioinformatics, 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. This book 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 Bioinformatics 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.

and the Table of Contents:

1) Introduction to DNA Sequencing
Stuart M. Brown
2) Quality Control and Data Processing
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
Philip 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 NGS to Detect Genome Sequence Variants
Jinhua Wang
12) ChIP-seq
Stuart M. Brown, Zuojian Tang, Christina Schweikert, and D. Frank Hsu
13) RNA-seq 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) 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