Detailed information about the course
Metabarcoding Pipeline Building (Mothur & R)
Mme Rachel Korn, UNIFR Dre Magdalena Steiner, UNIFR Prof. Louis-Felix Bersier, UNIFR
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)
24 - 30 April 2021
University of Fribourg, Perolles campus
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)
PhD students of the CUSO Microbilogie are eligible for the reimbursement of incurred travel expenses by train (half-fare card, and 2nd class).
The online reimbursement system is now in place, so once the course is over you will be able to request the reimbursement via MyCUSO, without sending the paperwork to me.
Please contact the coordinator of the doctoral program (microbiolgie(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. In case of overnight stay, please post the original tickets and original bills along with the reimbursement form to:
To register, please use your MyCUSO account!
REGISTRATION IS NOW OPEN ON THE ECOLOGY AND EVOLUTION PAGE
Deadline for registration: 18 April 2021
Priority is given to PhD students of the co-organising programs (each program has 4 places reserved) unitl 01 April 2021 - after this deadline places will be assigned on a first come, first serve basis, starting from the people in waiting list.
Free for participants enrolled in the CUSO Ecology & Evolution doctoral program.
In case of cancellations, before the deadline: free
Late cancellations or no-show: 100 CHF administrative fee
Other participants: please contact the program coordinator at ecologie-evolution(at)cuso.ch
|Deadline for registration|