Module 2.2 Introduction to genome assembly (outline)

Theme: Sequencing and assembly


2.2: Intro to genome assembly strategies

 

Time

Activity description

ILOs

9- 9.45

Lecture: “Introducing genome assembly strategies


  • Explain the basics of how raw sequencing reads are processed into genomes 
  • Explain why some organisms assemble into few contigs and others into a lot of contigs (when doing de-novo assembly) 
  • Understand the impact of read-length and base-calling quality for assembly 

 

 

Details

 

The overall aim of this lecture will be to provide an overview of the various ways in which a genome sequence (fasta-file) can be generated from raw reads. The major steps involved in de novo assembly will be covered (including topics such as OLC and de Bruijn graphs). We will discuss the impact of raw data choice and quality (i.e. short-reads vs long reads, paired-end reads and mate-pairs, base-calling quality vs assembly graphs). We will also mention the possibility of doing reference-based genome assembly.

 

Focus will be on contrasting different assembly strategies against each other, discussing pros and cons, and providing examples of where one strategy might be more suitable than another. 


 


Last modified: Monday, 25 March 2024, 10:53 AM