Book contents
- Frontmatter
- Dedication
- Contents
- List of insights
- Preface
- Notation
- Part I Preliminaries
- Part II Fundamentals of Biological Sequence Analysis
- Part III Genome-Scale Index Structures
- Part IV Genome-Scale Algorithms
- 10 Alignment-based genome analysis
- 11 Alignment-free genome analysis and comparison
- 12 Compression of genome collections
- 13 Fragment assembly
- Part V Applications
- References
- Index
13 - Fragment assembly
from Part IV - Genome-Scale Algorithms
Published online by Cambridge University Press: 28 September 2023
Book contents
- Frontmatter
- Dedication
- Contents
- List of insights
- Preface
- Notation
- Part I Preliminaries
- Part II Fundamentals of Biological Sequence Analysis
- Part III Genome-Scale Index Structures
- Part IV Genome-Scale Algorithms
- 10 Alignment-based genome analysis
- 11 Alignment-free genome analysis and comparison
- 12 Compression of genome collections
- 13 Fragment assembly
- Part V Applications
- References
- Index
Summary
Throughout the book we mostly assume the genome sequence under study to be known. In this chapter we look at strategies for how to assemble fragments of DNA into longer contiguous blocks, and eventually into chromosomes. This chapter is partitioned into sections roughly following the workflow of a de novo assembly project, namely, error correction, contig assembly, scaffolding, and gap filling. Algorithms working with de Bruijn graphs and overlap graphs are studied.
- Type
- Chapter
- Information
- Genome-Scale Algorithm DesignBioinformatics in the Era of High-Throughput Sequencing, pp. 308 - 330Publisher: Cambridge University PressPrint publication year: 2023