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6 Genome assembly
6.1 The problem of assembling genomes
6.2 Main algorithms for genome asssembly
6.2.1 Overlay, Layout, Consensus (OLS)
6.2.2 De Bruijn graphs
6.3 Main concepts of an assembly
6.3.1 Contigs, Unitigs, Scaffolds
6.4 A complete workflow for assembling genomes
6.5 Assessing genomes
6.5.1 Inspecting genome graphs
6.5.2 Genome completeness
6.6 Understanding genome difficulties
End of chromosomes
Erros
Lack of coverage
Heterozigozity
repeats