Module Overview

Determining the genome sequence of an organism can offer insights into its biology by allowing the identification of its gene complement and potentially regulatory sequences. Genome sequencing is frequently applied to pathogenic bacterial and fungal species with a view to understanding their pathogenicity and virulence. While historically genome assembly has been computationally intensive and a complex procedure, modern approaches can produce good results for small genomes using comparatively modest hardware. This module introduces concepts of genome assembly, assembly strategies and algorithmic approaches, assembly of small genomes, and automated annotations of prokaryotic genomes.

Learning Outcomes

After completing this module, participants will be able to:
  • Understand the terminology of genome assembly
  • Understand the benefits of different sequence types in de-novo assembly
  • Carry out contig assembly of small genomes using SPAdes
  • Understand how to assess a genome assembly
  • Carry out automated annotation of prokaryotic genomes using Prokka

Prerequisite Modules/Knowledge

  • Introduction to Linux
  • The HPC Cluster
  • Introduction to NGS

Course Schedule

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