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This course is provided by ECDC as part of the GenEpi-BioTrain programme.
It is open for enrolment for anyone interested in learning more about building basic bioinformatics workflows.

What is the aim of the training?

A key bioinformatics skill is using command-line tools for WGS analysis. Automation starts with small workflows but becomes sustainable through pipelines, requiring expertise in tools like Snakemake and Nextflow. Learning basic workflows is the first step toward building pipelines.

In this course, participants will set up basic workflows for raw read QC, genome assembly, and antimicrobial resistance genotyping. They will also explore how to extend these workflows with various bioinformatics tools and adapt them into scalable pipelines. Although workflow management systems such as Snakemake and Nextflow are not covered in this course, participants will gain relevant skills for the automation of bioinformatic analyses.

Who is the course for?

Beginners in bioinformatics and everyone interested in learning more about command-line tools and bioinformatics workflows. Participants are expected to have some familiarity with navigating and interacting with Unix terminals, creating and running simple bash scripts, and creating and working with virtual environments through the Conda ecosystem.

How long is the course?

Two live sessions will take place on Wednesday 19 and Friday 21 March from 09:00 to 12:30.

Will the course be recorded?

When you enrol to the course, you will also get access to the recordings after the live sessions. 

Can I get a certificate?

To get a certificate of completion, you need to attend at least one live session and to watch the recordings of the sessions you were not able to attend.