Course content
For mapping and exploring communities of both micro- and macro-organisms, high throughput sequencing (HTS) of environmental DNA has become a powerful suite of approaches. One approach to analyze organismal communities is to conduct HTS of a selected PCR-amplified marker (aka 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 (1) different sequencing techniques, (2) filtering and quality assessment of high throughput sequence data, (3) error correction and/or clustering of high throughput sequence data, and (4) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including multivariate community analyses, network analyses and 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. Applications of a wide suite of 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.
What will you learn?
You will learn about conceptual topics related to bioinformatics analyses of DNA-metabarcoding data and will be introduced to best practices. You will get experience in data processing using DADA2 and other programs.
How will we teach?
The entire course will run at Blindern, where we will have a mixture of lectures and hands on computer sessions.
Prior knowledge requisites?
Some programs, like DADA2, will be run in the R environment. Hence, 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.
Course organizers/lecturers:
Håvard Kauserud (UiO), Micah Dunthorn (UiO), Ramiro Logares (Barcelona), Anders Krabberød (UiO), Torbjørn Rognes (UiO)
Registration: Registration is now closed.
Credits: 3 ECTS
Contacts: Håvard Kauserud, University of Oslo, or Micah Dunthorn