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Lecture 03B
Genome assembly

Methodology

Date: Jan 23, 2024

This lecture delves into the computational algorithms used in genome assembly. It starts with the greedy algorithm as a foundation before introducing De Bruijn graphs as a modern approach. Students will explore how graph traversal techniques are used to extract contigs from assembly graphs. The session also covers SPAdes' methodology, emphasizing multi-sized graphs and paired-end reads.

Learning objectives

After today, you should have a better understanding of:

  1. Problem formulation of genome assembly.
  2. The greedy algorithm for genome assembly.
  3. De Bruijn graphs and their role in assembly.
  4. Graph traversal methods for extracting contigs.

Supplementary material

Relevant content for today's lecture.

Presentation

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