Some partial slides and exercises for the Livestock pangenomics: how to construct and exploit whole genome information summer school.
Organised at the Università Cattolica del Sacro Cuore in Piacenza by Paolo Ajmone Marsan and John Williams.
Some lecture notes for
- Introduction to pangenomics
- Genome assembly and pangenome graphs
- Pangenome visualisation
- Assessment of the pangenome
- Assessment of the pangenome part 2
- Finding functional associations within livestock pangenomes
Some associated exercises for
- Hands on pangenome assembly of a chromosome
- Identification of small and structural variants
- Aligning sequencing reads to a pangenome
- Using a pangenome to identify a known functional variant
Much of the data and intermediate files is available.