Detailed information about the course
Title | [REPORT À 2021] Metabarcoding Pipeline Building |
|
Dates | 05. - 09.10. 2020 |
|
Organizer(s) | Ms Rachel Korn, UNIFR Dr Magdalena Steiner, Agroscope, Wädenswil |
|
Speakers | Prof. Gerhard Thallinger, Technical University of Graz Rachel Korn, UNIFR Dr Magdalena Steiner, Agroscope Wädenswil |
|
Description |
|
|
Program | Schedule (preliminary) Introduction to metabarcoding · DNA extraction · Internal controls (positive, negative) · Primer choice (16S, 18S, ITS…) · NGS technologies (Illumina, IonTorrent, PacBio) · Sequencing variants, data formats · FASTQ format · Reference databases (SILVA, greengenes, PR2, …) · Amplicon sequence variants (ASV/ESV) vs. operational taxonomic units (OTU) Quality control
Pipeline: OTU construction (mothur)
Pipeline: ASV construction (dada2)
Analysis (R, main packages: phyloseq & vegan)
|
|
Location |
University of Fribourg, Boulevard de Pérolles 90, building 21/22, rooms G314 & G514 1700 Fribourg |
|
Evaluation | Full attendance and active participation.
Make sure to sign the attendance list each and every day! |
|
Information | When? Where? 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 (4 for each program) |
|
Expenses | Reimbursement:
PhD students of the CUSO Microbiologie 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: Andrea BsharyCUSO Microbiologie e-mail: [email protected]
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 | Registration will open in January. To register, please use your MyCUSO account! |
|
Places | 16 |
|
Deadline for registration | ||
Joint activity |