IN-BIOS9000 – Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics

Schedule, syllabus and examination date

Choose semester

Course content

Changes in the course due to coronavirus

Autumn 2020 we plan for teaching and examinations to be conducted as described in the course description and on semester pages. However, changes may occur due to the corona situation. You will receive notifications about any changes at the semester page and/or in Canvas.

Spring 2020: Teaching and examinations was digitilized. See changes and common guidelines for exams at the MN faculty spring 2020.

 

 

The course provides knowledge of sequencing technologies and hands-on experience with the analysis of data from several sequencing platforms and for various applications. The two main applications that will be covered are de novo genome assembly and variant calling (SNPs and structural variants), while other aspects like control of quantity and quality of data will also be included. Furthermore, the course will show how to use statistical genomics to analyse features of annotated genomes.

Learning outcome

After completing this course, you will:

  • understand the differences, benefits and drawbacks of the most current high throughput sequencing (HTS) technologies, and be able to decide which platform to use in what way for the different applications of HTS
  • be able to evaluate data quality and quantity as well as perform bioinformatics analysis, both on the command-line and through web-based frameworks, with data tailored towards applications like genome assembly and variant calling
  • know the algorithms and statistical methods involved in sequence alignment, mapping, assembly and variant calling
  • understand how to apply statistical methods to analyse relationships between annotated features on genomic tracks
  • be able to report on bioinformatics analysis in such a way that the methods used and steps taken are transparent, thus enhancing reproducibility
  • be aware of, and know to deal with, the ethical and data-sensitivity issues surrounding sequencing data derived from human subjects
  • be able to critically evaluate, validate and judge the results of bioinformatics analysis of HTS experiments in terms of underlying assumptions, reliability, sensitivity and specificity, and evaluate their value for answering biological questions

Admission

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.

A maximum of 30 students total for IN-BIO5000 and IN-BIO9000 combined.

Ranking:
1) PhD candidates who have the course as a part of their approved PhD plan and are associated with the NORBIS research school.
2) PhD candidates who have the course as a part of their approved PhD plan.
3) Master students at the Faculty of Mathematics and Natural Sciences who have the course approved in their study plan.
4) Master students at the Faculty of Mathematics and Natural Sciences.
5) Others

Prerequisites

Recommended previous knowledge

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.

Teaching

This is an intensive course covering six weeks in the autumn semester.

The course will start with 2 continuous weeks of lectures and hands-on exercises Monday to Friday each week, from 9.00 to 17.00. During the evenings the students are supposed to self-study for 2 hours by reading articles etc.

The following 4 weeks the students will work on a student project and prepare an oral presentation, which forms part of the exam. They will also read and prepare for the final written exam.

On Thursday in the sixth week the students will present their student work orally. On Friday in the sixth week there will be a written exam.

80% attendance on lectures and exercises is required to be allowed to take the exams.

Examination

There will be a 2-hour written exam, and the project work will be evaluated based on an oral presentation. Both exams have to be passed in the same semester. 80% attendance is required to be allowed to take the exams

Examination support material

No examination support material is allowed.

Language of examination

The examination text is given in English, and you submit your response in English.

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Explanations and appeals

Resit an examination

Students who can document a valid reason for absence from the regular examination are offered a postponed examination at the beginning of the next semester.

Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.

Withdrawal from an examination

It is possible to take the exam up to 3 times. If you withdraw from the exam after the deadline or during the exam, this will be counted as an examination attempt.

It will also be counted as one of your three attempts to sit the exam for this course, if you sit the exam for one of the following courses:

IN-BIOS5000 – Genome Sequencing Technologies, Assembly, Variant Calling and Statistical GenomicsINF-BIO5121 – High Throughput Sequencing technologies and bioinformatics analysis (continued)INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis (continued)

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Facts about this course

Credits

10

Level

PhD

Teaching

Every autumn

No teaching autumn 2019

Examination

Every autumn

Teaching language

English