Detailed information about the course

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Long-Read Sequence Analysis


14-15 March 2023

Lang EN Workshop language is English
Responsable de l'activité

Grégoire Rossier


Dr. Grégoire Rossier, SIB


Dr. Gerrit Adriaan van Geest, SIB & UniBE

Dr. Marco Kreuzer, UNIBE

Dr. Alban Ramette, UNIBE



For the last few years, research in DNA and RNA has been dominated by short-read sequencing. Although this has revolutionized the way we answer biological questions, it has its limitations. One important limitation is read length. The invention of high-throughput long-read sequencing has enabled us to solve questions on genome assembly, haplotyping, structural variation and alternative splicing. In this course, the participant will get acquainted with the major long-read sequencing technologies (PacBio SMRT and Oxford Nanopore Technology), and get experience with hands-on work involving long-read data.

The training materials for this course are in its dedicated GitHub page. The course includes a Guest Lecture from Dr. Alban Ramette.



Schedule - CET time zone 

Day 1 - 9h to 17h

Morning: Introduction Server login = unix fresh up

Afternoon: Quality control and Read alignment Applications



Day 2 - 9h to 17h

Morning: Group Work

Afternoon: Group Work Presentations Application 





This course is addressed to people that are working with or will be working with long-read data.



Learning outcomes

At the end of the course, the participants are expected to:

-Understand the basics behind PacBio SMRT sequencing and Oxford Nanopore Technology sequencing

-Use the command line to perform quality control and read alignment of long-read sequencing data

-Be able to do differential isoform expression analysis or a repeat expansion analysis based on long-read sequencing data



Prerequisites Knowledge / competencies

This course is designed for anyone interested to work with long-read data and there is a requirement for basic UNIX knowledge.


You are required to bring your own laptop. Software installation instructions will be communicated before the course.





The course is not yet open to applications. Sign up to receive the notifications when a course opens for applications (usually 2 months before the start). Say you are a member of StarOmics by signing up.

Application/Cancellation deadline: 28 February 2023



Deadline for registration

For more information, please contact training(at)sib(dot)swiss

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