Viromics2026: Course description

Viromics - Big data analysis and interpretation (MMB019-9)

An advanced module of the Masters program in Microbiology at Friedrich-Schiller University of Jena.

Prerequisites

Before the first day of the Viromics module, please set up your laptop according to these instructions.

Purpose and contents of the class

Metagenomics of viruses, often referred to as viromics, is the study of viral communities in a sample or environment by directly sequencing and analysing their genetic material. Unlike approaches that rely on virus isolation or cultivation, viromics can capture both culturable and unculturable viruses, allowing the discovery of novel viruses and characterising whole communities.

In this class, you will learn how to analyse bacteriophage sequences using computational approaches. The workflow will cover:

Viromics workflow

Data (to be updated)

We will be using viromics sequencing data from Natia Geliashvili, a PhD student in the VEO Group. The samples came from a sediment/river microbial community, into which a target phage and its host were added. The samples were passed through a 0.22um filter and sequenced using Oxford Nanopore Technologies (ONT) long-read sequencing.

Course structure

The course combines short video lectures, selected readings from research papers, questions, and hands-on analysis of computational data. Each day you will work through these materials at your own pace, combining conceptual learning with practical exercises.

During the practical exercises, you will work with real viromics data and use a range of bioinformatics tools to analyse and interpret the data. The emphasis is not on scripting or running tools, but on understanding what they do, critically evaluating their output, and drawing biological conclusions. Some command-line and scripting skills are required and will be taught, and support is be available throughout the course.

Each day at 16:00, you will submit a short report (maximum one page) answering the questions from that day’s activities. From 16:00–17:00, we will discuss the day’s material and results together in a plenary session. Active participation in these discussions is an important part of the course and will contribute to your grade (see “final evaluation” below).

The final days of the course will be devoted to a mini-project, in which you will apply what you have learned during the course to develop a research question and design the appropriate bioinformatics analyses to to answer it. You will give a presentation about your project on Friday 11 September.

Final evaluation

Your final grade is based on an evaluation of three factors.

Statement on AI/Large Language Model use

Large language models (LLMs), such as ChatGPT, Le Chat, and Claude, are increasingly becoming part of the daily work of bioinformaticians. Nevertheless, we advise you not to use LLMs during the practicals of this course. This is not because they are never useful, but because using them may hinder your learning more than it helps. We want you to focus on understanding the concepts and analyses yourself. We provide scripts where you mainly need to modify parameters and interpret the results, and discussing questions with your fellow students or the TAs is more useful for your learning than asking an LLM.

If you decide to use LLMs, you must include a sentence explaining how you used them in your daily report.