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?