Detailed information about the course

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Bioinformatics and statistics for metabarcoding studies in environmental microbiology and ecology


9-10 December 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:

 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




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.





9 & 10 December 2019

9:00 - 18:00



University of Neuchâtel

Faculty of Sciences

Rue Emile-Argand 11

UniMail, building B

Room B316 (room Florapolis)




Marta Bellone


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:


 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


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)




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