BIO9905MERG1 – Bioinformatics for Environmental Sequencing (DNA metabarcoding)
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.
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. You will be introduced to important analytical bioinformatics approaches from processing of raw sequence data to establishment of the OTU/sample matrix.
You will be introduced to high throughput sequencing (methods and concepts) and how the DNA metabarcoding sequence data can be analyzed further. 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.
Admission to the course
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.
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.
A project report will be compulsory and must be submitted two weeks after the course. The report will be marked as passed/not passed.
Examination support material
All examination support material is allowed.
Grades are awarded on a pass/fail scale. Read more about the grading system.