ForBio and UiO/IBV course: Bioinformatics for environmental DNA sequencing

For mapping and exploring communities of both micro- and macroorganisms, high throughput sequencing of environmental DNA has become a powerful approach. One can either analyze the total DNA content to obtain knowledge about which genes are present (DNA metagenomics) or sequence a selected PCR amplified marker (DNA metabarcoding) to obtain information about the taxonomic composition. We will focus on the latter approach in this course. The students will be introduced to important analytical bioinformatics approaches from processing of raw sequence data to establishment of the OTU/sample matrix and retrieval of taxonomic identity of the sequences.

Important themes will be (1) filtering and quality assessment of high throughput sequence data, (2) error correction and/or clustering of high throughput sequence data, and (3) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including network analyses. Applications of a wide suite of tools will be presented, including VSEARCH and DADA2.

Overlapping courses:
The course overlaps with ForBio/Tromsø Museum, UiT course "DNA Metabarcoding: Data processing and interpretation". Both courses will provide conceptual insights of the workflow going from raw data to a data matrix but will introduce the students to different approaches.  While overlapping thematically, they will introduce algorithmically different solutions, implemented as different software tools: Obitools (Tromsø course) and DADA2, VSEARCH and swarm (at the UiO course). The latter suite of tools is often used in studies of microbial/fungal communities.


There will be a team of internal UiO and external teachers.

Main teaching: Torbjørn Rogners (University of Oslo) and Ramiro Logares (Institute of Marine Sciences, Barcelona).

This course is registered at the University of Oslo as BIO9905MERG1 and amounts 5 ECTS (if the course report is submitted) and 3 ECTS (without a submission of course report). Course attendance certificates will be issued by ForBio for those participants who are not registered at the UiO.


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

Financial aid: Participation of the Norwegian-affiliated students/postdoctoral researchers will be covered by ForBio.  Other applicants will need to secure own funding to cover travel to Oslo, accommodation and subsistence for the course duration. There is no course fees. Please register for ForBio membership here.

Registration and selection process: Please fill in the online application here. ForBio reserves the right to give priority to the PhD students having their research focus on DNA metabarcoding applications. 



Recommended previous knowledge

Basic knowledge in molecular biology and DNA analyses. Basic knowledge in R and some insight in programming/scripting will be highly advantageous. 


The course combines lectures (before lunch) and computer labs after lunch each day.

This is an intensive course over five days (March 25-29).


A project report will be compulsory and must be submitted two weeks after the course.
The report will be marked as passed/not passed.

Grading scale

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

Explanations and appeals

Explanation of grades and appeals

For more information about the application/admission to the course contact Galina Gusarova  and for the questions regarding the course content: Håvard Kauserud and Galina Gusarova

Registration deadline is January 24, 2019.

Published Nov. 11, 2018 11:41 PM - Last modified Nov. 29, 2018 4:18 PM