Description
Book SynopsisNext-generation DNA and RNA sequencing has revolutionized biology and medicine. With sequencing costs continuously dropping and our ability to generate large datasets rising, data analysis becomes more important than ever. Next-Generation Sequencing Data Analysis walks readers through next-generation sequencing (NGS) data analysis step by step for a wide range of NGS applications.
For each NGS application, this book covers topics from experimental design, sample processing, sequencing strategy formulation, to sequencing read quality control, data preprocessing, read mapping or assembly, and more advanced stages that are specific to each application. Major applications include:
- RNA-seq: Both bulk and single cell (separate chapters)
- Genotyping and variant discovery through whole genome/exome sequencing
- Clinical sequencing and detection of actionable variants
- De novo genome assembly
Table of Contents
1. The Cellular System and The Code of Life. 2. DNA Sequence: the Genome Base. 3. RNA: the Transcribed Sequence. 4. Next-Generation Sequencing (NGS) Technologies: Ins and Outs. 5. Early-Stage Next-Generation Sequencing (NGS) Data Analysis: Common Steps. 6. Computing Needs for Next-Generation Sequencing (NGS) Data Management and Analysis. 7. Transcriptomics by Bulk RNA-Seq. 8. Transcriptomics by Single Cell RNA-Seq. 9. Small RNA Sequencing. 10. Genotyping and Variation Discovery by Whole Genome/Exome Sequencing. 11. Clinical Sequencing and Detection of Actionable Variants. 12. De Novo Genome Assembly with Long and/or Short Reads. 13. Mapping Protein-DNA Interactions with ChIP-Seq. 14. Epigenomics by DNA Methylation Sequencing. 15. Whole Metagenome Sequencing for Microbial Community Analysis. 16. What’s Next for Next-Generation Sequencing (NGS)?.
