Bioinformatics and statistics for metabarcoding studies in environmental microbiology and ecology

9-10 December 2019

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:

 09:00 – 11:00:  general introduction onto the applications of metabarcoding to scientific questions in ecology and to the main bioinformatics analyses techniques.

 11:00 – 11:20:  tea & coffee break

 11:20 – 13:00:  introduction to UNIX environment and bash scripting applied to large sequence file manipulation

 13:00 – 14:00:  lunch break

 14:00 – 16:30:  Illumina MiSeq raw reads quality trimming and pair-end merging – hands-on parallel computation

 16:30 – 16:50:  tea & coffee break

 16:50 – 18:00:  ASV/OTU clustering and taxonomic assignment

Day 2 – Alpha and Beta diversity:

 09:00 – 11:00:  introduction to the R software and to the vegan, dplyr and ggplot packages

 11:00 – 11:20:  tea & coffee break

 11:20 – 13:00:  alpha diversity: normalization, measure and statistical tests

 13:00 – 14:00:  lunch break

 14:00 – 16:30:  taxonomic composition: publication ready figures and statistical tests

 16:30 – 16:50:  tea & coffee break

 16:50 – 18:00:  beta diversity: testing effect of experimental factors and parameters on community composition

 18:00 – 18:15:  feedback and farewell

University of Neuchâtel

1 ECTS

Full attendance and active participation.

Make sure to sign the attendance list each and every day!

Reimbursement:

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:

 Marta Bellone 

 Doctoral Program in Ecology and Evolution

 University of Fribourg

 Chemin du Musée, 10

 CH-1700 Fribourg

NO reimbursement of your meal expenses.

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

Deadline for registration: November 24, 2019

Registration Fees: 

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

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