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Lecture 08
Read mapping

Date: Sep 19, 2024

DRAFT

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We'll explore the challenges of aligning millions of short reads to a reference genome and discuss various algorithms and data structures that make this process efficient. The session will focus on the Burrows-Wheeler Transform (BWT) and the FM-index, two key concepts that revolutionized read alignment by enabling fast, memory-efficient sequence searching. We'll examine how these techniques are implemented in popular alignment tools and compare their performance characteristics.

Learning objectives

What you should be able to do after today's lecture:

  1. Describe the challenges of aligning short reads to a large reference genome.
  2. Compare read alignment algorithms, including hash-based and suffix tree-based approaches.
  3. Explain the basic principles of the Burrows-Wheeler Transform (BWT) for sequence alignment.

Readings

Relevant content for today's lecture.

Presentation