Lecture 04
De novo genome assembly
Date: Sep 5, 2024
This lecture aims to provide a thorough understanding of de novo assembly techniques, their applications, and their crucial role in advancing genomic research.
Learning objectives¶
What you should be able to do after today's lecture:
- Explain the fundamental challenge of reconstructing a complete genome.
- Describe and apply the principles of the greedy algorithm.
- Understand and construct de Bruijn graphs.
Readings¶
Relevant content for today's lecture.
- Greedy algorithm
- de Bruijn
- JHU
- JHU2
- Why are de Bruijn graphs useful for genome assembly?
- Read mapping on de Bruijn graphs
- Galaxy
- Data science for HTS
- SPAdes assembler
- Online graph builder. Note that they use knode values.
Presentation¶
- View: slides.com/aalexmmaldonado/biosc1540-l04
- Live link: slides.com/d/KOit8yE/live
- Download: biosc1540-l04.pdf