Organizer: Australian BioCommons

Start: Thursday, 07 October 2021 @ 14:00

End: Thursday, 07 October 2021 @ 17:00

Timezone: AEDT

Contact: Melissa Burke (melissa@biocommons.org.au)

Country: Australia

Scientific topic: Genomics

Operations: Genome assembly

Description:

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:

  1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly
  2. Use genome assembly and polishing programs in Galaxy Australia
  3. Assess the quality of a genome assembly with and without a reference genome
  4. 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.

Apply here

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.

Event type:
  • Workshops and courses

Capacity: 50

Eligibility:
  • Registration of interest

Keywords: Hybrid genome assembly

WORKSHOP: Hybrid de novo genome assembly https://tess.elixir-europe.org/events/workshop-hybrid-de-novo-genome-assembly 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](https://github.com/fenderglass/Flye), [Pilon](https://github.com/broadinstitute/pilon/wiki), and [Unicycler](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595) 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](https://usegalaxy.org.au/), 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: 1. Describe how Nanopore and Illumina reads can be used together to produce a high quality assembly 2. Use genome assembly and polishing programs in Galaxy Australia 3. Assess the quality of a genome assembly with and without a reference genome 4. 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](https://training.galaxyproject.org/training-material/). **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](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html). 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. **[Apply here](https://hybrid-assembly.eventbrite.com.au/)** This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Melbourne Bioinformatics](https://www.melbournebioinformatics.org.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative). To hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to the Australian BioCommons’ eNewsletter. 2021-10-07 14:00:00 UTC 2021-10-07 17:00:00 UTC Australian BioCommons Australia Australia Genomics [] Melissa Burke (melissa@biocommons.org.au) [] [] 50 workshops_and_courses registration_of_interest Hybrid genome assembly