IN-BIOS5000 – Sequencing technologies, data analysis, and applications

Course content

The course provides knowledge of sequencing technologies and hands-on experience with the analysis of data from several current sequencing platforms and for various biological and medical applications. Tools, algorithms, and statistical methods for data analysis will be included, as well as data quality assessment and analysis reproducibility. The applications that will be covered may vary from year to year but will typically include de novo whole-genome assembly and variant calling. Other applications like RNA-Seq, ChIP-Seq, or metagenomics could also be covered.

Learning outcome

After completing this course, you will:

• understand the differences, benefits, and drawbacks of the current sequencing technologies, and be able to decide which platform to use in what way for the different applications
• be able to evaluate sequencing data quality and quantity
• know the tools, algorithms, and statistical methods involved in the data analysis
• be able to perform bioinformatics analysis with data tailored towards selected applications
• be able to report on the data analysis in such a way that the methods used and the 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 sequencing experiments in terms of underlying assumptions, reliability, sensitivity and specificity, and evaluate their value for answering biological questions

Admission to the course

Students who are admitted to study programmes at UiO must each semester register which courses and exams they wish to sign up for in Studentweb.

If you are not already enrolled as a student at UiO, please see our information about admission requirements and procedures.

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

Ranking:

1. PhD students who have the course as a part of their approved PhD plan and are associated with the NORBIS research school.
2. PhD students 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

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.

Overlapping courses

• 10 credits overlap with IN-BIOS9000 – Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics.
• 10 credits overlap with INF-BIO5121 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
• 10 credits overlap with INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
• 10 credits overlap with INF-BIO5120 – High Throughput Sequencing technologies and bioinformatics analysis (continued).
• 10 credits overlap with INF-BIO9120 – High Throughput Sequencing technologies and bioinformatics analysis (continued).

Teaching

This is an intensive course covering six weeks in the autumn semester of even-numbered years.

The course will start with two continuous weeks of full-day lectures and hands-on exercises.

The following four 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.

At the end of the sixth week the students will present their student work orally and take 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 must be passed in the same semester. 80% attendance is required to be allowed to take the exams.

Exams are only organized in the same semesters as the course is given.

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 course: IN-BIO9000, INF-BIO5121 – High Throughput Sequencing technologies and bioinformatics analysis (continued), INF-BIO9121 – High Throughput Sequencing technologies and bioinformatics analysis (continued)

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.

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.

More about examinations at UiO

• Use of sources and citations
• Special exam arrangements due to individual needs
• Withdrawal from an exam
• Illness at exams / postponed exams
• Explanation of grades and appeals
• Resitting an exam
• Cheating/attempted cheating

You will find further guides and resources at the web page on examinations at UiO.