This online workshop is hosted by Genomics Aotearoa and NeSI. The workshop will be taught from 10:00am-4:00pm NZT on the 26th of July 2023 and is for New Zealand researchers interested in learning to create and work with pangenome graphs.

This workshop will include:

- An introduction to pangenome graphs.

- Setup guide for using the tools and data in the workshop.

- Overview of the PGGB toolkit.

- Choosing parameters to construct a graph.

- QC

- Extracting variant data.

- Mapping short reads against a pangenome graph.

This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:

- Navigating files and directories.

- An understanding on full versus relative paths.

- Working with files and directories (examining files, creating, copying, moving and removing).

- Use a command line-based text editor such as nano.

If you lack the above skills, you can use these sites as a refresher:

- Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/

Setup

This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms - there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

You can view the workshop material, including the objectives and content here.

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Constructing Pangenome Graphs with PGGB