Introduction to Metagenomics Data Analysis of Microbial Communities

4-5-6 May 2026

Mme Corinne Dentan, CUSO StarOmics

Dre Valeria Di Cola, SIB

Dre Sarah Miéville, CUSO Microbiologie

Dr Laurent Falquet, UNIFR

M. Jeferyd Yepes-Garcia, UNIFR

This course introduces the complete metagenomics data analysis workflow, from raw data to downstream biological interpretation. It covers both targeted marker‑gene sequencing (16S) and whole‑genome shotgun (WGS) metagenomics. Participants learn about sequencing choices, quality control (QC), OTU/ASV processing, assembly and binning, and available tools for in‑depth analyses and publication‑ready results.

Learning Outcomes

Participants will be able to:

• Understand fundamental concepts in metagenomics
• Compare targeted (16S) vs. whole‑genome methods
• Perform QC and cleaning of raw sequencing data
• Navigate key databases and pipelines
• Evaluate pipeline outputs
• Identify appropriate downstream analysis strategies

Prerequisites

Knowledge:

• Basic R and UNIX skills
• Familiarity with RStudio (installing libraries, manipulating matrices/data frames, importing/exporting text files)

Technical:

• Personal laptop with up‑to‑date R and RStudio

Provisional schedule (09:00–17:00, CET)

Day 1 AM: Introduction + UNIX/R refresher

Day 1 PM: Sequencing options & QC (short/long reads)

Day 2 AM: 16S analysis with DADA2

Day 2 PM: 16S downstream analysis

Day 3 AM: WGS assembly/binning with nfcore‑mag

Day 3 PM: WGS downstream analysis

SIB activity page

UNIFR

This course is organized in collaboration with the CUSO doctoral programs in Microbial Sciences and StarOmics and the SIB

Reimbursements for CUSO Students: Train ticket, 2°class, half-fare from your institution to the place of the activity. Reimbursement of your travel tickets can be asked online through your MyCUSO. See HERE for the procedure. For any question concerning reimbursement please contact the CUSO Microbiology coordinator Sarah Miéville

Register on the SIB activity page and mention that you are a CUSO member.

10 places available for CUSO students (4 StarOmics + 6 Microbiology)

Registration deadline : 27.04.2026

Important informations :

• A waiting list will be prepared to ensure that there are no empty seats.
• For cancellations after the deadline of registration or no-show: 50 CHF administrative fee

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