Next-Generation DNA Sequencing Informatics

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. This book provides a thorough introduction to the necessary informatics methods and tools for operating NGS instruments and analyzing NGS data. The book also provides extensive reference to best-practice bioinformatic methods for the most commonly used NGS technologies and applications. The book 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.

1. Introduction to DNA Sequencing

2. History of Sequencing Informatics

3. Visualization of Next-Generation Sequencing Data

4. DNA Sequence Alignment

5. Genome Assembly Using Generalized de Bruijn Digraphs

6. De Novo Assembly of Bacterial Genomes from Short Sequence Reads

7. Genome Annotation

8. Using NGS to Detect Sequence Variants

9. ChIP-seq

10. RNA Sequencing with NGS

11. Metagenomics

12. High-Performance Computing in DNA Sequencing Informatics

Glossary

Index