Educators:
Nils Kleinbölting (BiGi), Daniel Wibberg (CAU), Anna-Maria Möller, Florian Kraft, Tassilo Wollenweber
Date:
7-9 July 2025
Location:
Düsseldorf & Online
Content:
The aim of this workshop is to familiarize participants with Long-Read sequencing technologies, its applications, and the best practice bioinformatics workflow. Participants will gain insights into how this technology facilitates the assembly of prokaryotic and eukaryotic genomes, focusing on establishing finalized genome sequences.
The workshop will begin with an introduction to PacBio and Nanopore sequencing, covering its principles and differences from other sequencing methods. We will discuss the evolution of Long-Read technology and its current role in the sequencing landscape. Participants will also explore various applications, including genome assembly, real-time sequencing and transcriptomics, illustrated by case studies highlighting its effectiveness in research and clinical settings. A central component of the first workshop day is a practical part in which a sequencing library is first prepared and then used for real-time sequencing.
On the second day, students will start getting familiar with the Linux operating system and receive an introduction to the command line, with a focus on file and directory management. No prior bioinformatics knowledge is required
On the third, bioinformatics workflow associated will be outlined, covering the standard processes from raw data acquisition to final genome assembly. Participants will learn about key tools such as Minimap2, Canu, and Flye, as well as the advantages and pitfalls of Long-Read sequencing, including long read lengths and potential error rates.
The hands-on component will guide participants through a typical workflow, starting with data preprocessing and quality control in the de.NBI cloud environment. They will practice sequence alignment and genome assembly, followed by basic genome annotation techniques.
Learning goals:
This workshop aims to teach basic skills and best practices to researchers working with Long-Read data. The full course will include all necessary steps from an introduction to PacBio and Nanopore sequencing (1), raw sequencing data to finalized genomes (2) with a de novo assembly and (3) with re-sequencing and mapping to a reference.
Prerequisites:
This workshop is intended for PhD students and postdocs with molecular biology background in genomics. Good understanding of command line tools is a plus, but not required. The 2nd day will offer an introduction to Linux and the command line.
Tools:
minimap2, canu, pilon, guppy, porechop, medaka, poretools, nextstrain, quast,
Keywords:
Nanopore sequencing, PacBio sequencing, genome assembly, genomics,
Contact:
Daniel Wibberg d.wibberg@fz-juelich.de
