Genome Sequence Analysis

Course content

The course focuses on second-generation sequencing technology, its wide applications, and the Bioinformatics analysis of produced sequencing data. Newer sequencing technology (third generation) will also be overviewed. Strategies for analyzing second generation sequencing data will be covered, including quality control of raw sequencing data, mapping reads to a reference genome and contemporary downstream data analyses. Downstream analyses will be performed using UNIX command tools and R statistical programming enviroment and will include gene/transcript expression quantification, differential expression analysis and de novo transcript reconstruction from RNA sequencing data and variant/genotype calling from whole-genome DNA sequencing data. Based on authentic biological samples, mutants will be identified by variant calling. Genetic experiments that relate the identified mutants to a biological phenotype will be conducted.


MSc Programme in Biochemistry
MSc Programme in Biology
MSc Programme in Biotechnology
MSc Programme in Molecular Biomedicine

Learning outcome


  • Second generation sequencing technology
    • Library construction (theoretical level)
    • Sequencing by synthesis
    • Bridge amplification
    • Base calling
    • Newer developments (third generation)
  • Applications of second generation sequencing technology
    • Overview of how second generation sequencing can be used / adapted to answer various biological questions
    • Whole-genome DNA sequencing
    • RNA sequencing
  • Analysis strategies and workflows for second generation sequencing data
    • Filtering and quality evaluation of raw reads
    • Mapping of sequencing reads onto a reference genome
    • Sequencing coverage
    • Variant and genotype calling from whole-genome DNA sequencing data
    • Gene/transcript expression quantification, de novo transcript reconstruction and differential expression analysis using RNA sequencing data
  • Basic knowledge of the various statistical/computational approaches and tools used when dealing with sequencing data and how and why these differ between sequencing applications
  • Familiarity with of state-of-the-art statistical and computational approaches for dealing with whole-genome sequencing data for variant calling and RNA-sequencing data for gene transcript expression quantification and differential expression analysis
  • Basic knowledge of the issues and potential problems with second generation sequencing data and how to deal with those
  • Basic knowledge of impact of study designs and how to avoid and deal with batch effects 
  • Genomic annotation of sequencing data and genome browsers


  • Identify differentially expression of gene transcripts between biological samples of different types or conditions
  • Identify mutations in an experimental sample by variant calling
  • Design and carry out genetic experiments to relate identified variants with mutant phenotypes


  • Critically evaluate results of second generation sequencing experiments from different perspectives (molecular biology, bioinformatics, genetics)
  • Independently analyze and interpret whole-genome DNA sequencing data and RNA-sequencing data

Lectures, theoretical and practical exercises, colloquia.

Notes, articles.
See Absalon.

BSc in Biology, Biochemistry, Molecular Biomedicine or equivalent.

Continuous feedback during the course of the semester
Peer feedback (Students give each other feedback)
7,5 ECTS
Type of assessment
Continuous assessment
Type of assessment details
Participation in the theoretical and practical exercises and colloquia.
The course uses continuous assessment with five different assignments. Students will work on each assignment in groups and present their results in written or oral form in group or individually, depending on the assignment. The assignments are weighted with the following percentages: 10%, 30%, 15%, 30%, 15%, for assignments 1, 2, 3, 4, 5, respectively.
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
One internal examiner

The reexam will be held as an oral exam (30 minutes) with 1 hour preparation time (all aids allowed).


Criteria for exam assessment

See Learning Outcome.

Single subject courses (day)

  • Category
  • Hours
  • Class Instruction
  • 12
  • Preparation
  • 131
  • Theory exercises
  • 21
  • Practical exercises
  • 42
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 2
The number of seats may be reduced in the late registration period
Study Board for the Biological Area
Contracting department
  • Department of Biology
Contracting faculty
  • Faculty of Science
Course Coordinator
  • Robin Andersson   (5-79766970754769707635727c356b72)

Robin Andersson, Olaf Nielsen, Anders Albrechtsen.

Saved on the 10-05-2023

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