Educators:
Nils Kleinbölting (BiGi), Daniel Wibberg (CAU), Tobias Busche, Christian Rückert, Levin Joe Klages (Omics CF NGS and CeBiTec Technology Platform, Bielefeld University)
Date:
30 June - 2 July 2026
Location:
Bielefeld University
Content:
The aim of this workshop is to familiarize participants with Oxford Nanopore sequencing technologies, its applications, and the best practice bioinformatics workflow. Participants will gain insights into how this technology facilitates the assembly of prokaryotic genomes and metagenomes, focusing on establishing finalized genome sequences and MAGs.
The workshop will begin with an introduction to 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 first half of 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 second half of the second day and on the third day, 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 Dorado, Minimap2, and (meta)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 basecalling, 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 and a few insights into metagenomics with ONT.
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 Nanopore sequencing (1), raw sequencing data to finalized genomes and MAGs (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 a molecular biology background in (meta)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, pilon, dorado, porechop, medaka, quast, metabat2, Checkm2, GTDBtk, prokka, bakta, bwa2, metagenomics-tk
Keywords:
Nanopore sequencing, genome assembly, genomics, metagenomics
Contact:
Daniel Wibberg (
Registration:
Will open soon