Genome assembly using the command line

This hands-on practical workshop is an introduction to processing high throughput sequencing data and de novo genome assembly.

Learning Objectives

  • Choosing the appropriate sequencing platform and methods
  • Choosing and using the appropriate genome assembly tools
  • De novo assembly of a demonstration dataset
  • Techniques for post-assembly quality assessment and initial genome annotation


  • Refresher to common CLI commands and computer basics
  • Sequencing platforms and library preparations
  • Overview of de-novo genome assembly workflow and common tools
  • Quality control and data filtering
  • De novo assembly
  • Annotation and visualisation of assembled genome

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