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In this course, we will focus on DNA-metabarcoding. The students will be introduced to important bioinformatics approaches used during DNA metabarcoding, ranging from processing of raw sequence data to establishment of the final OTU/sample matrix and retrieval of taxonomic identity of the sequences. Important themes will be
- (a) different sequencing techniques
- (b) filtering and quality assessment of high throughput sequence data
- (c) error correction and/or clustering of high throughput sequence data
- (d) taxonomic annotation of high throughput sequence data.
We will also touch upon some further downstream analyses, including evolutionary placement of short-read sequences onto reference phylogenies. We will also focus on long-read sequencing and how this can be used in DNA-metabarcoding. Several tools will be presented, including DADA2, SWARM and VSEARCH. There will be a few guest lectures, focusing on specific topics such as long-read metabarcoding and decontamination of metabarcoding data. In addition, some case studies will be presented. Further instructions and a selection of articles will be provided to course participants some weeks before course start.
Some basic knowledge in R will be very helpful. Knowledge in (UNIX) command-line will also be advantageous. Otherwise, general knowledge about DNA sequencing and organismal biodiversity will make it easier to follow.
The course corresponds to 3 ECTS credits.
The course is supported by the Digital Life Norway Research School and there are a limited number of travel grants available for our members.
Course organizers/lecturers
Håvard Kauserud (UiO), Micah Dunthorn (UiO), Ramiro Logares (Barcelona), Anders Krabberød (UiO), Torbjørn Rognes (UiO)
For more information, contact Håvard Kauserud at haavarka@ibv.uio.no