main page — CS 594 Algorithms of Bioinformatics
Unit 4: Assembling Genomes
This unit covers the problem of assembling genomes from sequencing reads:
- fragment assembly problem
- overlap graphs
- de Bruijn graphs
- assembly algorithms
Material
- slides
- Video 4-1 (2025-11-27, 25:18):
Exploding Newspapers, DNA Sequencing Technology
- Video 4-2 (2025-11-27, 19:47):
De-novo sequence assembly, Overlap Graphs
- Video 4-3 (2025-11-27, 39:39):
de Bruijn graph assembly, Hierholzer’s algorithm
Further sources
- Compeau & Pevzner, Bioinformatics Algorithms: An Active Learning Approach, Chapter 4
- Nebel, Algorithmen der Bioinformatik
- Ismaili Alaoui, Plump, Wild, Space-Efficient Hierholzer: Eulerian Cycles in O(m) Time and O(n) Space, SOSA 2026
- Gifford, Foundations of Computational and Systems Biology – 6. Genome Assembly