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Genome Assembly DNASeq Lab III

Meg Staton edited this page Sep 28, 2016 · 10 revisions

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

Readings

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

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