Detailed information about the course
Metabarcoding Pipeline Building
20-24 April 2020
Rachel Korn, UNIFR
Dr Magdalena Steiner, Agroscope, Wädenswil
Prof. Gerhard Thallinger, Technical University of Graz
Rachel Korn, UNIFR
Dr Magdalena Steiner, Agroscope Wädenswil
Metabarcoding is a rapidly evolving technique that identifies DNA from a set of often unknown organisms and reveals microbial communities in unprecedented taxonomical resolution by using universal PCR primers and high-throughput sequencing. It increasingly gains importance in almost all fields of biological and medical sciences. Its wide application range includes biodiversity assessment and monitoring, diet analysis, reconstruction of paleocommunities and more. The processing of metabarcoding data requires a broad range of skills at the interface of molecular biology, bioinformatics, biostatistics and biology/ecology.
In this workshop the participants will be introduced to the workflow of microbiome research targeting the 16S and 18S rRNA gene: preceded by an overview of the full process, this course is aimed at the analysis of high-throughput sequencing data with open-source and cross-platform software (mothur and R/bioconductor packages) from the raw reads to the visualization of results. Theoretical content will be visualized and strengthened by practical exercises. Participants will practice during the workshop on prepared data sets.
A basic statistic knowledge as well as basic skills in R are a precondition for this workshop. The participants are required to bring their own notebooks with the software already installed. For this, a Docker image containing all necessary software will be provided to guarantee architecture and version control.
Introduction to metabarcoding
Pipeline: OTU construction (mothur)
Pipeline: ASV construction (dada2)
Analysis (R, main packages: phyloseq & vegan)
University of Fribourg, Chemin du Musée 10, 1700 Fribourg
Full attendance and active participation.
Make sure to sign the attendance list each and every day!
20 to 24 April 2020
University of Fribourg,
Boulevard de Pérolles 90, building 21/22, rooms G314 & G514, 1700 Fribourg
The course is organized in collaboration with the CUSO Microbiology, CUSO StarOmics and UNINE Organismal Biology Doctoral Programs.
16 places in total, equally shared among the co-organising programs (4 for each program)
Phone: +41 (0)26 300 88 91
PhD students of the DPEE are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class). Please send the original tickets along with the reimbursement form to:
Department of Biology
University of Fribourg
Chemin du Musée 10
NO reimbursement of your meal expenses
Regarding reimbursement of accommodation, please contact the coordinator of the doctoral program (ecologie-evolution(at)cuso.ch) BEFORE the beginning of the course. NO reimbursement of accommodation without the coordinator of the doctoral program agreement prior of the course.
Registration is open until 29 March 2020.
Priority is given to PhD students of the co-organising programs (each program has 4 places reserved) unitl 8 March 2020 - after this deadline places will be assigned on a first come, first serve basis, starting from the people in waiting list.
To register, please use your MyCUSO account!
|Deadline for registration||29.03.2020|