14  Genome assembly

14.1 The problem of assembling genomes

14.2 Main algorithms for genome asssembly

14.2.1 Overlay, Layout, Consensus (OLS)

14.2.2 De Bruijn graphs

14.3 Main concepts of an assembly

14.3.1 Contigs, Unitigs, Scaffolds

14.4 A complete workflow for assembling genomes

14.5 Assessing genomes

14.5.1 Inspecting genome graphs

14.5.2 Genome completeness

14.6 Understanding genome difficulties

• End of chromosomes

• Erros

• Lack of coverage

• Heterozigozity

• repeats