Hybrid de novo genome assembly – Nanopore and Illumina

June 22, 2022 -
21 Bedford Street, North Melbourne VIC, Australia


Hybrid de novo genome assembly – Nanopore and Illumina

Workshop date/time (Melbourne time): Wednesday 22nd June 10am-1pm

Lead trainer

Grace Hall (Melbourne Bioinformatics, The University of Melbourne)

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

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

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 or working through this material is sufficient for attendance.


For further information, email bioinformatics-training@nullunimelb.edu.au.