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?