Overview

High-throughput sequencing (HTS) technology has revolutionized the field of biology, including genomics, epigenomics, transcriptomics, and metagenomics. HTS allows numerous DNA molecules to be sequenced simultaneously, rather than one at a time, enabling unprecedented speed and scale. By generating vast amounts of genetic data rapidly and cost-effectively, HTS provides large and comprehensive datasets that can yield deeper biological insights.

In this 3-day course, we will introduce the most widely used HTS technologies. Using different datasets, we will practice quality control, alignment of reads to a reference genome, and visualization of sequencing data.

What will you learn in practice?

In the era of AI-assisted bioinformatics, knowing which commands to run is no longer enough. This hands-on course focuses on the reasoning behind sequencing data analysis: choosing appropriate approaches, evaluating results, identifying potential problems, and interpreting data in a biological context.

Participants will work with real-world datasets and research examples, perform analyses themselves, discuss their decisions in groups, and present their findings. AI tools may be used as assistants, but participants will be expected to critically evaluate their suggestions and justify their analytical choices.

Audience

This course is designed for PhD students, postdoctoral researchers, and other researchers in the life sciences from academia and industry who are working with or planning to work with high-throughput sequencing data.

It is particularly suited to researchers who want to develop not only practical skills, but also the ability to critically evaluate sequencing analyses, make informed analytical choices, and interpret results in their biological context.

Learning outcomes

At the end of the course participants should be able to:
* Distinguish the advantages and limitations of HTS technologies and their applications in omics
* Select appropriate HTS technologies based on experimental design needs
* Apply quality control (QC) measures to HTS datasets to assess data integrity and identify potential issues before downstream analysis
* Describe the concept and purpose of sequence alignment and differentiate between global and local alignment strategies
* Perform read alignment to a reference genome using appropriate tools
* Analyze alignment outputs to assess accuracy and identify potential issues
* Generate visualizations of HTS data using tools such as IGV
* Evaluate visualized outputs to interpret biological insights and validate results
* Critically evaluate computational and AI-assisted analysis suggestions and justify analytical choices based on the biological question and characteristics of the data.

Prerequisites

Knowledge / competencies

This course is part of the Omics Data Analysis learning path. To get the most out of this course, you should meet the learning outcomes of First Steps with UNIX in Life Sciences
or the e-learning course UNIX Fundamentals. Upon completion of this course, you may wish to attend the Single-Cell Transcriptomics with R and Introduction to Bulk RNA-Seq: From Quality Control to Pathway Analysiscourses.

In case of doubt, evaluate your Unix skills with this quiz.

Technical

Software requirements will be communicated before the course.

Application

Registration fees for academics are 300 CHF and 1500 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close on 16/10/2026 or as soon as the places will be filled up. Cancellation after 16/10/2026 will not be reimbursed. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

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 working days.

Venue and Time

The course will only be streamed online.

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

Precise information will be provided to the registered participants in due time.

Additional information

Coordination: Grégoire Rossier, SIB Training group.

A Certificate of Attendance will be sent provided you were present at the course, whereas a Certificate of Achievement recommending 0.75 ECTS will be sent provided you passed the exam.

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.

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 [email protected].