Overview

In many domains of life sciences, Next Generation Sequencing (NGS) methods have become an indispensable part of research and clinical practice. Due to its massive throughput and versatile applications, like genomics, transcriptomics, epigenomics and metagenomics, it supports knowledge generation in a broad range of applications. However, sequencing experiments result in (very) large datasets, with specific file formats, which can make the downstream analysis challenging.

In this course, you will learn about the background of most used sequencing technologies and about the concepts of quality control and read alignment. You will put this knowledge into practice by performing hands-on exercises in which you will learn how to perform such analysis with the command line. To make interpretation of the analysis results easier, you will learn how visualize the output using a genome browser. After performing all analysis steps in a guided manner, you will work on a mini project to learn how to apply the learnt skills more independently.

If you have some experience with the command line, and are ready to get started with NGS analysis, this course is for you.

Are you getting curious? All course materials can be found on the dedicated GitHub page.

Audience

This course is intended for life scientists who are already dealing with NGS data and would like to be able to start analysing them.

Learning outcomes

At the end of the course participants should be able to:

understand the basics of the different NGS technologies
perform quality control for better downstream analysis
align reads to a reference genome
visualize the output

Prerequisites

Knowledge / competencies:

Participants should have a basic understanding of working with the command line on UNIX-based systems like Linux or Mac. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module or attend one of the "First Steps with UNIX in Life Sciences".

Technical:

Participants should bring their own computers. 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 as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 11/11/2025. Cancellation after this date will not be reimbursed.

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.

Venue and Time

This course will take place at the University of Bern.

This course will start at 9:15 and end around 17:15. Precise information will be provided to the participants on due time.

Additional information

Coordination: Monique Zahn, SIB Training group.

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.

NGS - Quality Control, Alignment, Visualisation