Overview

This course will cover the metagenomics data analysis workflow from data generation to downstream analysis. Participants will explore the tools to manage, share, analyze and interpret metagenomics data. The content will include issues of data quality control and how to process the data until publication.

Both targeted marker-gene (e.g., 16S) and whole-genome shotgun (WGS) approaches will be covered. Discussions will also explore considerations when selecting the sequencing options (long or short reads), exploring targeted data to OTUs or ASVs, assembling and binning metagenomics data, the analyses that can be carried out, and what downstream analyses options and tools are available.

Audience

This course is addressed to life scientists (PhD or postdocs) who are working in the field of metagenomics and are currently in the early stages of data preparation or data analysis.

Learning outcomes

At the end of the course, the participants are expected to:

Know the concepts of metagenomics
Understand and compare the two main methods (targeted vs whole genome)
Perform QC and cleaning of the data
Comprehend about various databases and pipelines
Evaluate the results of the pipelines
Discover downstream analysis options

Prerequisites

Knowledge / competencies

This course is designed for beginner users. For the practical sessions we require a basic understanding of the Unix command line and the R statistics packages. Participants might want to work through these free tutorials before attending the course:

R, beginner level (Rstudio, how to install a library, matrix and data frame manipulation, import and export data from text files). Test your R skills with the quiz here, before registering.

Technical

You are required to bring your own laptop with the latest R and RStudio versions installed.

Schedule - CET time zone

The course will start at 9:00 and end around 17:00.

Day1am: General introduction to the topic and Unix/R reminder

Day1pm: Sequencing options and QC (short/long reads)

Day2am: 16S analysis with DADA2

Day2pm: 16S downstream analysis

Day3am: WGS assembly/binning with nfcore-mag

Day3pm: WGS downstream analysis

Application

The registration fees for academics are [XXX] CHF and [XXX] CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications close on 30/04/2025. Deadline for free-of-charge cancellation is set to 23/04/2025. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place at the University of Fribourg.

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants in due time.

Additional information

Coordination: Valeria Di Cola.

We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

Introduction to Metagenomics Data Analysis of Microbial Communities