11 – 14 April 2022

Due to the COVID-19 outbreak, this course will be held online



Long-read genome sequencing technologies offer the opportunity to assemble highly contiguous genome sequences for a huge spectrum of organisms, including telomere-to-telomere human chromosomes, fully closed bacterial chromosomes and plasmids, and even entire viral genomes in single reads. A wide variety of tools exist to process long-read sequencing data, from basecalling through to genome assembly and polishing. Each of these has been developed to optimise the accuracy of the resulting genome assemblies, either in hybrid with paired short-read data, or using long reads alone.


This course will introduce participants to a range of methods to complete the steps required to process raw Oxford Nanopore Technologies sequencing data into a fully assembled, polished and quality-controlled genome assembly, both with and without accompanying short reads, and with and without a reference genome. Over four days, we will include a combination of both theoretical background and practical application using model viral and bacterial datasets, concluding with a full run-through of the assembly, polishing and quality control pipeline at each course participants’ own pace.




Target audience and assumed background

This course is intended for researchers interested in learning the background and practical techniques involved in genome assembly using Oxford Nanopore Technologies data. Both beginners and more advanced users are welcome.  Some background in navigating the command line would be useful, but we will cover the needed essentials throughout the hands-on sessions.



Learning outcomes


     Learn the advantages and disadvantages of long-read sequencing


     Understand the steps involved in genome assembly using long read data


     Gain practical experience in choosing and using the optimal tools for a variety of dataset types, including microbiome, bacterial, viral and mammalian




Monday. 2-8 pm Berlin time

Session 1: Introduction, basecalling and demultiplexing




We will start with a general introduction to sequencing and assembly using Oxford Nanopore Technologies sequencers. Participants will be introduced to the theory of how nanopore sequencing works, its advantages and disadvantages compared to short-read sequencing and other long-read sequencing technologies, and how raw nanopore sequencing data is formatted.




Practical sessions will include using current gold standard basecalling tools to transform raw nanopore signal data into DNA sequence (including an example of multiplexing/demultiplexing in nanopore sequencing), and how to quality control and filter your basecalled sequencing reads.




COst overview

Package 1


480 €

Cancellation Policy:




> 30  days before the start date = 30% cancellation fee


< 30 days before the start date= No Refund.




Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.