Schedule for the Assembly module

Day 1

  • brief overview of the module
  • assembly exercise
  • lecture: “Principles and problems of de novo genome assembly”
  • tutorial: exploring De Bruijn graphs
  • tutorial: assembly with velvet
  • starting overnight assemblies

Day 2

  • basic metrics of the assemblies performed so far
  • mapping reads back to the velvet assembly
  • visualisation of mapped reads in IGV
  • assembly improvement using REAPR
  • evaluating the other assemblies

Day 3

  • comparing assemblies to the reference using Quast
  • lecture: “Assembly, before and after”
  • comparative evaluation of assemblies
  • rounding up: which assembly was best?