Genome Assembly DNASeq Lab III

Overview

• (finishing up from last time) Filtering variants and determining their effect
• Become familair with the algorithms underlying genome assembly
• Practice assembling reads into a genome
• Generating quality metrics for a genome assembly

Concepts to Know

• What does de novo mean?
• Depth vs Coverage for NGS reads
• What are some things that make genome assembly a difficult problem to solve?
• What is are the main differences in OLC vs De Bruijn graph? Which uses less memory?
• What is a k-mer and how do you select one for your assembly?
• What is a Euler path?
• De bruijn graphs can have spurs, bubbles and frayed ropes - what biological phenomenon cause each?
• General overview of steps to go from raw reads to a genome assembly
• What types of metrics would you use to assess the quality of a genome assembly?

Materials

• Assembly Practical
• Assembly Slides
• Finish up variant calling

Readings

Ekblom and Wolf. A field guide to whole-genome sequencing, assembly and annotation