Eukaryotic genome assembly using Pacbio (Hifi and clr) and Hi-C


14 – 18 November 2022

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




Eukaryotic genomes may be composed of many repeats. Long reads sequencing technologies can span most of those repeats and produce genome assemblies with unprecedented contiguity. Further, sequencing technologies such as PacBio HiFi give us assembly contiguity and base accuracy. Chromatin conformation capture reads (Hi-C) bring the final information to scaffold assemblies into chromosomes.
This course will introduce the audience to a spectre of methods which are present in a usual assembly workflow, starting from raw data and finishing with a fully assembled genome. We will see how to manipulate raw reads, analyse their quality, how to run different assembly algorithms, how to run Hi-C scaffolding algorithms and how to analyse assembly quality.


Structured over five days, this course consists of both theoretical and practical aspects which are intertwined through each day. The presented theoretical foundation will be applied on small eukaryotic datasets.



Target audience


This course is intended for researchers interested in learning the theory and practice on how to perform de novo eukaryotic genome assembly using Pacific Biosciences Long Reads and Hi-C data. Both beginners and more advanced users will find useful information in this course. Course attendees must have a laptop with either macOS or any Unix version. Background in using mentioned operating systems via the command line is highly desirable. We will, however, cover the essentials throughout the hands-on sessions.


Learning outcomes


  • Understanding PacBio HiFi (mostly), PacBio CLR and Hi-C data.
  • Understanding the concepts of de novo genome assembly.
  • Obtaining practical experience on using state-of-the-art tools for de novo assembly and assembly quality assessment.



Monday - Classes from 2 to 8 pm Berlin time


-       Genomes


-       Sequencing technologies


-       Genome assembly


                -    Hands on: Introduction to Linux – manipulating reads files



COst overview

Package 1

530 €


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.