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Lecture 06B
Read mapping

Methodology

Date: Feb 13, 2025

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.

Learning objectives

After today, you should have a better understanding of:

  1. The purpose of reference-based mapping.
  2. Hash-based methods for handling introns.
  3. Suffix arrays for efficient substring searches.
  4. Burrows-Wheeler Transform (BWT) string compression.
  5. FM-index for efficient substring searches.
  6. Splice-aware mapping with seed-chain-extend strategy.

Supplementary material

Relevant content for today's lecture.

Presentation

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