Read alignment: exact matching

The goal of read alignment is to determine the location in the reference genome or transcriptome where each read originated. This information is important for many downstream applications, such as variant calling (identifying differences between the reads and the reference genome) and transcriptome analysis (identifying which genes are being transcribed and at what levels).

There are many algorithms that are used for aligning reads to a genome. In this section, you will be introduced to the very basic exact matching algorithms that search for the exact assurance of a specific string of characters (the "pattern") within a larger body of text (the "text").

Read alignment and why it's hard

Naive exact matching

Practical: Matching artificial reads

Practical: Matching real reads

Boyer-Moore basics

Boyer-Moore: putting it all together

Diversion: Repetitive elements

Practical: Implementing Boyer-Moore

Problems to solve

Try to solve these problems after completing the section. Some of them may be challenging :)

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