Metabarcoding: from Lab to Bioinformatics
On-site in Tartu 1-7 August 2022
High-throughput metabarcoding methods have become a routine analysis tool in biodiversity research and ecology in general. This course will cover the principles of metabarcoding workflow, from the laboratory analyses to bioinformatic analyses of the high-throughput sequencing data.
Laboratory work includes steps for sample preparation, DNA extraction, PCR and sequencing library preparation. The practical sessions are supplemented with theoretical lectures.
Hands-on metabarcoding data set analyses will mostly follow PipeCraft 2 pipeline (user-friendly graphical user interface software for non-bioinformaticians) but basics of command-line interface and usage of high-performance clusters will be also covered.
| Focus area: | Biology, Ecology, Mycology, and Microbiology | Coordinating unit at UT |
Chair of Mycology, Institute of Ecology and Earth Sciences |
| Study Field: | Biology, Mycology, Microbiology, and Ecology | Course Leader | Dr. Niloufar Hagh-Doust, Research fellow at University of Tartu |
| Format | Practical and theoretical sessions | Location | Tartu, Estonia |
| Course dates: | 1-7 August 2022 | Apply by: | 19 June 2022 |
| ECTS: | 4 (evaluation method: participants will be asked to prepare a 2 page report) | Fee: | 450 € |
| Study group | MSc/PhD and Post-doc | Language | English |
Lecturers:
- Prof. Leho Tedersoo, University of Tartu
- Prof. Urmas Kõljalg, University of Tartu
- Dr. Sten Anslan, University of Tartu
- Dr. Vladimir Mikryukov, University of Tartu
- Dr. Kessy Abarenkov, University of Tartu
- Dr. Niloufar Hagh-Doust, University of Tartu
- Dr. Heidi Tamm, University of Tartu
- Ali Hakimzadeh, University of Tartu
Monday
- Opening lecture
- Lectures on the basic concepts of DNA extraction, PCR and primer selection, metabarcoding and sequencing technologies and necessary steps to build up metabarcoding libraries. There will be an opportunity for software installation troubleshooting after the lecture.
Tuesday
- Practical sessions in the laboratory including DNA extraction and PCR.
Wednesday
- Practical lab sessions on preparing metabarcoding libraries.
- Bioinformatics sessions with a lecture by Sten Anslan plus software installation troubleshooting if necessary.
Thursday
- Practical sessions on bioinformatic data analysis.
Friday
- Bioinformatics practical sessions
- Lecture on Publishing to GBIF/UNITE/PlutoF
- Closing lecture.
The participants can take part in cultural group activities after the study sessions.
Participants will be expected to have a basic understanding about molecular biology.
The target audience are Master and PhD students, early career researchers (post-docs), or senior researchers, either from Industry or Academia, with no or little prior knowledge on metabarcoding techniques. This workshop is mainly aimed for students and researchers with a background in ecology, biodiversity research or community biology who wish to use molecular tools for their research.
Entry requirements:
- Online application form
- Motivation letter (up to 1 page) that demonstrates the applicant’s motivation to participate, his/her expectations about the programme, how participation in the summer programme relates to his/her studies and interests, and how the applicant plans to use the gained experience and knowledge in the future.
- Transcript of academic records
- Copy of passport
PS: Only complete applications including all annexes submitted by the deadline will be considered for selection.
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Understanding the main concepts, potentials and limitations of metabarcoding techniques.
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Knowledge of the laboratory procedures necessary for metabarcoding.
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Ability to set up the working environment for bioinformatic analysis.
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Knowledge of key bioinformatic procedures for metabarcoding sequence data analyses.
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Understanding of the full cycle of data management and publishing.
Two weeks prior to the start of the programme an information file will be sent to all participants. This file contains the daily schedule and relevant contact information of the programme managers.
Students are responsible for their travel, accommodation and travel insurance (visa arrangements if needed) from their home country to Tartu and back to their home country. It is recommended to visit the Tartu Welcome Centre website and arrival and housing section to find accommodation opportunities.
The University of Tartu will offer 20 tuition waivers (scholarships) altogether for citizens of Ukraine for all summer courses. It will cover the course fee and cultural programme. Accommodation and daily expenses are not included.
The selection process is going to be based on the motivation letter. In order to apply for the scholarship please submit your application to the summer course and upload a motivation letter (no longer than approx 1 A4 page).
