Course Outline

  1. Introduction
  2. Biochemistry background and sequencing by synthesis
  3. Base calling for second-generation sequencing
  4. Third-generation technologies: Nanopore and Pacific Biosciences
  5. Genome assembly I: Formulation
  6. Genome assembly II: Read overlap and De Bruijn graphs
  7. Long-read assembly: a case study
  8. Haplotype phasing
  9. Alignment I
  10. Alignment II
  11. RNA-Seq I: Introduction
  12. RNA-Seq II: Quantification vs the EM algorithm
  13. RNA-Seq III: Differential expression
  14. Single-cell RNA-Seq I: Technology and challenges
  15. Single-cell RNA-Seq II: Dimensionality reduction, clustering and computing representatives
  16. Single-cell RNA-Seq III: Dimensionality reduction, clustering and computing representatives
  17. Single-cell RNA-Seq IV: Differential expression
  18. Cancer genomics
  19. Project presentation