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Week 6 - Alignment

  1. Introduction
  2. Learning Objectives
  3. Lecture Material
  4. Assignment

Introduction

This week, we will focus on aligning reads to a reference. This is a crucial first step in almost all OMICS procedures. Upon completion, we will have an alignment file that indicates where each read aligns to a reference genome and how it does so.

We will continue to use the Snowflake Yeast Datset.

Learning Objectives

By the end of this week, students should be able to:

  • Understand the Burroughs-Wheeler Alignment (BWA) algorithm and its applications.
  • Differentiate between BWA and other alignment algorithms (like BLAST).
  • Understand why we should not put large result-files into git repos.
  • Understand the purpose of generating alignment indexes.
  • Use samtools to view and count the number of aligned reads.
  • Use samtools flagstat to summarize an alignment result.
  • Understand the important fields of a SAM format.

Assignment

For this assignment, you will use BWA to align Illumina reads from a sequencing of multi-cellular snowflake yeast. In future weeks these results will be identify variants that may be associated with multicellularity. Finally, you will interpret the results of the alignment.