Long-read sequence analysis

Date 14 - 15 March 2022
Speaker(s) Geert van Geest
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 28 Feb 2022
City Bern
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


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.


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


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.

Schedule - CET time zone

Day 1 - 9h15 to 17h15


  • Introduction
  • Server login = unix fresh up


  • Quality control and Read alignment
  • Applications

Day 2 - 9h15 to 17h15


  • Group Work


  • Group Work
  • Presentations


The registration fees for academics are 120 CHF and 600 CHF for for-profit companies.

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.

Deadline for free-of-charge cancellation is set to 28/02/2022. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place at the University of Bern. No online streaming is currently planned. Please be aware that to comply with recent federal and cantonal recommendations, you will most probably have the obligation to present a COVID certificate to be able to attend the course. Take this into consideration before applying to this course.

It will start at 09:15 CET and end around 17:15 CET. Precise information will be provided to the participants in due time.

Additional information

Coordination: Valeria Di Cola

We will recommend 0.5 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.