De novo genome assembly

A module in the fall 2016 edition of INF-BIOx121

Slides:

• Introduction to the assembly module
• Principles and problems of de novo genome assembly
• De novo assembly using velvet

Practicals:

• Schedule for the Assembly module
• Assembly using velvet
• Mapping reads to an assembly and visualising the results
• Assembly improvement using REAPR
• Assembly using SPADES
• Assembly using CANU
• Assembly using miniasm+racon
• Comparing assemblies to the reference
• Mapping PacBio and MinION reads using bwa
• Sources of programs, scripts, datafiles etc

Content of the etherpad