Long-read Sequence Analysis

Overview

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 and Dr. Pamela Nicholson.

Audience

This course is addressed to anyone working with or interested in 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

You should meet the learning outcomes of: First Steps with UNIX in Life Sciences or the e-learning course UNIX Fundamentals.

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

Technical

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

Schedule

See Course schedule

Application

The registration fees for academics are 200 CHF and 1000 CHF for for-profit companies.

While participants are registered on a first come, first serve basis, exceptions may be made to ensure diversity and equity.

Applications will close as soon as the places will be filled up, but not later than 19/02/2025. Deadline for free-of-charge cancellation is set to 19/02/2025. 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 days.

Venue and Time

This course will take place at the University of Bern.

It will start at 9:15 CET and end around 17:15 CET.

Precise information will be provided to the participants before the course.

Additional information

Coordination: Diana Marek, SIB Training Group

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.