Hybrid de novo genome assembly – Nanopore and Illumina

2 August 2023 -
21 Bedford Street, North Melbourne VIC, Australia


Hybrid de novo genome assembly – Nanopore and Illumina

Workshop outline

Most modern bioinformatic analyses are not possible without high-quality reference genomes. They are the backbone that supports current and future discoveries, and our collection of complete genome sequences are one of humanity’s greatest achievements. Performing de novo assembly is easier than ever thanks to advances in long read sequencing and platforms such as Galaxy which enable bioinformatics workflows for non-coders. In this tutorial we will use the web-based analysis platform “Galaxy” to create a high-quality assembly of a Bacillus Subtilis strain. The software tools “Flye” and then “Pilon” will be used to perform the assembly and subsequent error correction to improve the accuracy of assembled contigs. You will learn how to will visualize input read sets and the assemblies produced at each stage and assess the quality of the final assembly. The training material used in this workshop is freely available here.

Tools Used 

Galaxy, Flye, Pilon

Lead trainer: Grace Hall

(Melbourne Bioinformatics, The University of Melbourne)

Learning objectives

By the end of this training, participants will be able to:
  • Understand how Nanopore and Illumina reads can be used together to produce a high quality genome assembly
  • Be familiar with genome assembly and polishing programs
  • Be able to perform de novo assembly using Nanopore and Illumina reads!


This FREE workshop is available to staff and students at The University of Melbourne and its affiliated institutes only. You must register for this event using an affiliated institutional email address or your registration may be cancelled.

Prerequisites and Requirements

This workshop does not require any previous experience with working with sequencing reads. However, this training workshop will be conducted using Galaxy. Therefore previous experience navigating the Galaxy platform is required as the workshop will not include introductory content on how to use the platform. Attendance at a previous Galaxy workshop (sign up to the workshop on July 18th) or working through this material is sufficient for attendance. This is an in person, hands-on workshop and attendees must bring their own laptops to the workshop . No software needs to be installed for this workshop and no programming experience is necessary. The following is required:
  • Access to internet via uniwireless or Eduroam
  • Web browser (Firefox or Chrome recommended)
  • Participants should register for a Galaxy Australia account using their institutional email address


If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements: We recommend that following our eventbrite page if you wish to be alerted when we release new workshops for registrations. If you require any further information, please contact Melbourne Bioinformatics at: bioinformatics-training@nullunimelb.edu.au
LAST RUN: June 22, 2022