Detailed information about the course
Bioinformatics and statistics for metabarcoding studies in environmental microbiology and ecology
9-10 décembre 2019
|Responsable de l'activité||
Dr Guillaume Lentendu, UNINE
Dr Guillaume Lentendu, UNINE
During the last decade, environmental sequencing has become a standard tool to monitor biodiversity for both micro- and macro-organisms. Following the development of high-throughput sequencing, a myriad of tools have been developed to efficiently process the ever increasing amount of sequence data produced. Target amplification of environmental DNA, also known as metabarcoding, is the most common and up-to-date technique used to assess the diversity of target organisms in the environment and is applied to a wide range of organisms, from bacteria, fungi and protists, to plant and insects.
During the courses, the participants will learn how to use bash and R scripting language for efficient processing of meta barcoding and biodiversity datasets. No previous knowledge of bash is needed, but basic R knowledge is requested.
The course will be organised on two days:
Day 1 – From raw reads to OTU table:
Day 2 – Alpha and Beta diversity:
University of Neuchâtel
Full attendance and active participation.
Make sure to sign the attendance list each and every day!
No previous knowledge of bash is needed, but basic R knowledge is requested. Ideally, a previous attendance of an introductory course to R is recommended.
The course will take place in a computer room of the University of Neuchâtel. The students will use the provided computers (one computer per student with every software needed for the course already installed) and example datasets to realize all the bioinformatic and statistic practical duties.
The participants could bring there own computer, but should have all software already installed (A list with links of sotware to be installed can be provided upon request). No support to installation and configuration of software on personal computers will be provided.
If a participant wants to analyze his/her own metabarcoding dataset, he/she should contact the course instructor beforehand.
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:
NO reimbursement of your meal expenses.
CUSO PhD students: through your MyCUSO account.
Other participants (non-CUSO PhD students, thus including post-docs, etc...): use the icon "registration" at top of page and the last gray box "non-CUSO student" ("personne hors myCUSO").
Priority is given to PhD students from the CUSO Doctoral Programs in Ecology & Evolution and the Interuniversity doctoral program in Organisma Biology (DPOB).
Registration is open at https://www.unine.ch/dp-biol/home/program/courses2019/Metabarcoding2019.html
Free for participants enrolled in the Interuniversity doctoral program in Organisma Biology (DPOB) or in the CUSO Ecology & Evolution doctoral program.
Other participants: please contact the program coordinator at ecologie-evolution(at)cuso.ch
|Deadline for registration|