About the course
For mapping and exploring communities of both micro- and macroorganisms, high-throughput sequencing of environmental DNA has become a powerful approach. One can either analyse 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 bioinformatic approaches, from processing raw sequence data to creating the OTU/sample matrix.
Learning outcomes
After the course, participants will:
- Understand the differences and strengths of different sequencing platforms, including short- and long-read technologies.
- Know how to perform filtering and quality assessment steps on environmental sequencing data
- Know how to perform error correction and clustering steps on environmental sequencing data
- Know how to taxonomically annotate environmental sequencing data
- Understand different downstream analyses that can be applied to environmental sequencing data, including multivariate community analyses, network analyses and evolutionary placement of sequences onto reference phylogenies
- Use a wide suite of bioinformatics tools, including DADA2, Swarm, and VSEARCH.
Teaching
There will be required reading before the course. The course combines lectures and computer labs each day. This is an intensive five-day course.
Target group
Priority will be given to PhD students and postdocs. MSc students may be considered if space is available and if they have sufficient background in bioinformatics.
Language
English
Credits
5 ECTS
Assessment
A three-page project report is compulsory and must be submitted two weeks after the course. The report will be marked as pass/fail.
BIOCORE will provide a certificate of participation upon successful completion of the course.
Teachers
- Håvard Kauserud, Department of Biosciences, University of Oslo
- Anders Krabberød, Department of Biosciences, University of Oslo
- Ramiro Logares, Institut de Ciències del Mar (CSIC)
- Micah Dunthorn, Natural History Museum, University of Oslo
Admission and application
Course fee
There is no course fee. However, students are responsible for their own travel, housing, and food.
Eligibility and prerequisites
Students must have a background in DNA analyses and bioinformatics, including basic knowledge of R and some insight into programming/scripting. Students must bring a laptop that can run the bioinformatics analyses.
How to apply
University of Oslo students should apply through the university course enrolment system. All other students can apply through BIOCORE.
<A link to the registration form will be provided soon>
BIOCORE Membership
We encourage all course applicants to become Associate Members of BIOCORE to receive updates and information about future events.
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