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Week 7 - Alignment Continued

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

Introduction

Last week, we focused primarily on short-reads against a large genome. However, this week, we will focus on aligning long reads in the presence of deletions and repeats. While these problems are general, they are common when sequencing the integrated HIV proviral genome. This is due to viruses that create deletions during the integration process and the 3' and 5' Long Terminal Repeats.

Learning Objectives

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

  • Utilize minimap2 for long read alignment.
  • Distinguish between non-primary alignments and supplemental alignments in SAM/BAM.
  • Interpret SAM/BAM files that contain alternative alignments.
  • Practice creating the required files for IGV with the HIV genome.
  • Use IGV to visualize non-primary alignments and supplemental alignments.

Assignment

Complete the in-class activities and use a PR to commit your notes to exercises/{user}/wk07/notes.md. Catch up on any previous assignments.

Project

In the next class we are going to discuss pipelines like Snakemake and NextFlow. Many of you have projects that already have well-tested pipelines. nf-core is an organization that maintains a wide array of these pipelines. Explore their website and see if one fits your project. Discuss it in your project Readme.