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Computationele Biologie

Chapter 03: How do we assemble genomes?

Na de deadline zal de correctheid en de computationele complexiteit (tijd en geheugen) van de volgende oefening geëvalueerd worden op basis van peer review:

  • Reconstruct a string from its k-mer composition (benchmark)
Title Class progress
K-mer composition
Reconstruct a string from its genome path
Construct an overlap graph from a collection of k-mers
Construct a de Bruijn graph from a string
Construct a de Bruijn graph from a collection of k-mers
Find an Eulerian cycle in a graph
Find an Eulerian path in a graph
Reconstruct a string from its k-mer composition
Find a k-universal circular string
Generate all maximal non-branching paths in a graph
Generate contigs from a collection of k-mers

  K-mer composition

Submit

  Reconstruct a string from its genome path

Submit

  Construct an overlap graph from a collection of k-mers

Submit

  Construct a de Bruijn graph from a string

Submit

  Construct a de Bruijn graph from a collection of k-mers

Submit

  Find an Eulerian cycle in a graph

Submit

  Find an Eulerian path in a graph

Submit

  Reconstruct a string from its k-mer composition

Submit

  Find a k-universal circular string

Submit

  Generate all maximal non-branching paths in a graph

Submit

  Generate contigs from a collection of k-mers

Submit