Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics fall 2018

Note: for previous course editions (INF-BIO9121 and INF-BIO5121), check out this website.

Lecture slides

Lecture slides
This page is updated after each lecture/Module.

Teaching materials

Link to Etherpad
List of further suggested papers, can be found here.

Home exam

Link to home exam


This is the webpage for the fall 2018 edition of the credited courses IN-BIOS5000 (master level) and IN-BIOS9000 (Ph.D. level) offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO) and funded by NORBIS.

This course consists of two weeks, of lectures and practicals, and a final take-home exam, plus a written exam on the course material and the reading material.


Course days are usually from 9:15 to 17:00 (teachers may stay longer if requested), some lectures, mostly hands-on exercises. All materials for lectures and practicals will be linked from the schedule below.

The schedule will appear here early in August and will link to the webpages with the material taught (these links are added as the course progresses).

Room location:

Day Room Morning (09:15-12:00) Afternoon (13:00-17:00)
Week 43
Mon. Oct. 22 Shell Update on NORBIS
Fundamentals of Molecular Biology
HTS & applications
Illumina sequencing
PacBio technology
Pizza evening
Tue. Oct. 23 Postscript Oxford Nanopore technology
Library preparation
Experimental design
Basic file formats
Wed. Oct. 24 Shell Pre-processing of HTS data Algorithms
Thu. Oct. 25 Java Algorithms De novo assembly
Dinner @1800 hrs in Olivia, Aker brygge
Fri. Oct. 26 Java De novo assembly De novo assembly
Week 44
Mon. Oct. 29 Shell De novo assembly De novo assembly
Tue. Oct. 30 Postscript Variant calling Variant calling
Wed. Oct. 31 Python Variant calling Variant calling
Thu. Nov. 01 Python Statistical genomics Statistical genomics
Fri. Nov. 02 Python Statistical genomics Statistical genomics
Week 48
Thu. Nov. 29 TBA Oral exam Oral exam
Fri. Nov. 30
14:30 hrs
Store fysiske
lesesal Fysikkbygningen
Written exam

Room location:

Ole-Johan Dahls hus location: Google maps

  • Shell: room 1456 Informatics building (Ole-Johan Dahls hus)
  • Postscript: room 2458 Informatics building (Ole-Johan Dahls hus)
  • Java: room 2423 Informatics building (Ole-Johan Dahls hus)
  • Python: room 2269 Informatics building (Ole-Johan Dahls hus)

Dinner on Oct 25

NORBIS sponsored dinner will be on Oct 25 at 1800 hrs in Olivia, Aker Brygge at Google maps

Exam location:

Written exam will take place on Nov 30 at 1430 hrs (2 hour exam) in Store fysiske lesesal Fysikkbygningen


  • We recommend that participants should have a basic understanding of molecular biology as provided by an introductory course in bioinformatics, molecular biology, or genetics.
  • No formal background in computer science is required, however, students must have a basic understanding of the unix shell. Students should take an introductory unix course beforehand if they do not have these skills.

Computers/laptops, internet access, and UiO user account

All students must bring a laptop with either a Windows (Windows 7 or more recent), Unix/Linux, or OS X (i.e. an Apple computer) operating system.

  • The computer should not be more than 2-3 years old
  • It should be possible to connect the computer to the UiO wireless network
  • You must have modern internet browser installed (Chrome, Firefox, Safari, …)
  • You must have a valid UiO user account and must be able to log onto a computer on the UiO network
    • If you are unsure if you have a UiO user account and a valid password, you should try to log in using as described here. If you are unable to log in, try the hints you find here.
    • Instructions (in Norwegian) about how to find your user name and get a new password can be found here.
  • We advise to bring an external mouse, and do not rely on touchpad/trackpad only

If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact the course coordinator (see contact details on this page) as soon as possible, and at least one week before the start of the course.

Curriculum and suggested reading

The curriculum consists of a set of scientific articles. The exam will contain questions on the material presented in these papers on the material covered during the course. Specific details of the curriculum, and a list of further suggested papers, can be found here.


Link to exam information at UiO

The exam for this course will be:

  • a written exam on the course and curriculum, time and place to be announced
  • an individual, home exam combined with an oral examination of the home exam time, and place to be announced. Students will present their work to two-three teachers, followed by some questioning (20-30 minutes in total). This home exam will be handed out to all participants during the last course day.

NOTE Both exams have to be passed to earn study credits.

NOTE 80% attendance is required to take the final exam.

Written exams from previous years

  • 2016 (exam only)
  • 2015 (with information on how the grading was done)
  • 2014 (exam only)

Contact information

  • Arvind Sundaram (Course coordinator) - e-mail: arvind.sundaram - at
  • Course administration/registration - e-mail:


  • Arvind Sundaram (AS, Bioinformatician, Norwegian Sequencing Centre, Oslo University Hospital)
  • Ave Tooming-Klunderud (AT, CEES, Faculty of Mathematics and Natural Sciences, University of Oslo)
  • Gregor Gilfillan (GG, Researcher, Norwegian Sequencing Centre, Oslo University Hospital)
  • Ivar Grytten (IG, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)
  • Karin Lagesen (KL, Section for Epidemiology, Norwegian Veterinary Institute)
  • Ragna Breines (Coordinator, NORBIS)
  • Thomas Haverkamp (KL, Section for Epidemiology, Norwegian Veterinary Institute)
  • Timothy Hughes (TH, Researcher, NORMENT , Oslo University Hospital)
  • Torbjørn Rognes (TR, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)