ℹ️ Please Note
You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 16 held in March 2025, and certificates are only issued to participants who attended the live webinar sessions.
Introduction
Welcome to the virtual training on "Introduction to building basic bioinformatics workflows"!
This course aims at providing you with skills to create and maintain workflows for automating routine bioinformatics tasks.
Description
An important skill in bioinformatics is the ability to install and use command line tools to perform analysis of whole genome sequence data. For the purpose of performing routine bioinformatics tasks associated with WGS-based public health surveillance, automation plays a vital role. The first step towards automation is to set up a basic workflow for small-scale use. Small-scale workflows are easy to maintain and can be developed by a small number of people. However, the use of such workflows depends on the involvement of developers. A sustainable solution is to convert a workflow into a pipeline. Creating and configuring bioinformatic pipelines is somewhat complex and requires expertise in workflow management systems such as Snakemake and Nextflow. Learning how to set up basic workflows is a precursor to learning how to build pipelines.
In this course, participants will learn about basic workflows and how to set them up. Participants will set up their own simple workflow to produce raw read QC reports, whole genome assemblies and basic antimicrobial resistance genotyping. Participants will be given a brief introduction on how to extend their workflow with additional bioinformatics tools, and will be given inspiration on how to advance their workflows into pipelines.
Intended audience
The target audience for this training is mainly beginners in bioinformatics, who 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 (see Prerequisites).
What you will not learn
In this virtual training, participants will not learn how to use the Unix terminal, how to code, and what bioinformatics tools or commands do. To these purposes, please explore the already available GenEpi-BioTrain virtual trainings freely available on the ECDC Learning Portal. Additionally, participants will not learn how to use workflow management systems like Nextflow and/or Snakemake.
Outline of sessions
The two sessions take place on 19 and 21 March 2025 at 09:00-12:30 (CET) on each day.
As with all GenEpi-BioTrain Virtual Trainings, the webinars will be recorded and you will be able to access the recordings at any time, provided you are enrolled in the course.
