It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality.
In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly.
All analyses will be performed using Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.
Date/time: 2 - 5pm AEDT/ 1 - 4pm AEST/ 1:30 - 4:30pm ACDT/ 11am - 2pm AWST, Thursday 7 October 2021
Lead Trainer: Grace Hall, Melbourne Bioinformatics
Learning outcomes
By the end of this workshop you should be able to:
Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly
Use genome assembly and polishing programs in Galaxy Australia
Assess the quality of a genome assembly with and without a reference genome
Assemble an unknown, previously undocumented genome to high-quality using Nanopore and Illumina reads
The workshop will NOT provide an introduction to the basics of Galaxy. If you would like to learn about this topic there are several tutorials available via the Galaxy Training Network.
Who the workshop is for
This workshop is for Australian researchers who are or will perform hybrid genome assembly as part of their projects.
To get the most out of the workshops you must have experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. It is recommended that you complete the tutorial Galaxy 101 for Everyone.
No programming experience is required.
How to apply
This workshop is free but participation is subject to application with selection. Applications close at 11:59pm AEST Wednesday 29 September 2021.
You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 1 October 2021. Successful applicants will be provided with a Zoom meeting link closer to the date.
Applications have closed
The training materials from this workshop are available via Zenodo.
This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
To hear when registrations open for other events, please subscribe to the Australian BioCommons’ eNewsletter.
Cover image: Courtesy Melbourne Bioinformatics