Plant genomics: chloroplast genome assembly using Galaxy Australia

April 21, 2021 - 1-4pm
Online via Zoom

Workshops

Plant genomics: chloroplast genome assembly using Galaxy Australia

Join us to step through genome assembly using chloroplast sequencing data and the Galaxy Australia web platform.  

It is becoming increasingly practical to use large genomic data sets to answer research questions in plant biology, but it can be difficult to know where to start. In this workshop, you will perform a genome assembly using chloroplast sequencing data and the Galaxy Australia web platform. You’ll have the opportunity to try out the workflows on the same or other data, using the free Galaxy platform and its tools.

Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The material covered in this workshop is freely available through the Galaxy Training Network.

The workshop will be held via Zoom and involve a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators.

Lead trainer: Dr Anna Syme, Bioinformatician, Australian BioCommons, Melbourne Bioinformatics, University of Melbourne.

Anna has a long history as a research scientist and has recently worked at the Royal Botanic Gardens Victoria. Her work on the Bioplatforms Australia project, Genomics for Australian Plants, and her current Australian BioCommons role sees her contributing to workforce transition of researchers working with genomic data.

Learning objectives

By the end of the workshop you should be able to:

  • assemble a chloroplast genome from a test dataset of Oxford Nanopore long sequencing reads
  • polish the assembly with short Illumina sequencing reads
  • view the assembly in a genome browser and an assembly graph viewer
  • describe how common tools can be combined to produce a workflow for genome assembly.

Who the workshop is for

This workshop is suitable for Australian researchers with an interest in using Galaxy Australia for genome assembly. The workshop requires some prior knowledge of genome assembly and the basics of using Galaxy Australia.

If you are new to these topics we recommend that you work through the following tutorials in advance:

Additional tutorials on genome assembly can be found on the Galaxy Training Network.

How to join

The workshop is free but places are strictly limited and registration requires an Australian institutional email address.

 

The workshop is presented by the Australian BioCommonsMelbourne Bioinformatics and Galaxy Australia with the assistance of a network of facilitators from around Australia.

This event is part of a series of bioinformatics training events. If you’d like to hear when registrations open for other events, please subscribe to the monthly Australian BioCommons newsletter.