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Using the HPC to run jobs, December 2023


The Genomics England Research Environment provides access to a High Performance Cluster (HPC) where you can access our genomic and clinical data and run large-scale analyses on these, using pre-installed bioinformatics tools, your own code and imported tools and software. This training introduces the HPC, including the compute and the queues available. We will show you how to access the available tools, including interactive coding tools, via the HPC, and how to run jobs using them. We will also cover bringing in tools and software from outside of the RE.

This training will be taught by our experts, including our HPC squad who create and maintain the cluster, and our bioinformaticians, who develop, install and work with the tools and workflows on the HPC.


13.30 Welcome and introduction
13.35 What is the High Performance Cluster?
13.50 Why use the HPC?
13.55: Queues and nodes available on the HPC
14.05: How to create and monitor jobs on the HPC
14.15: Tools and software available and how to load them
14.25: Interactive coding tools
14.35: Bringing in your own tools and software
14.45 Questions

Learning objectives

After this training you will be able to:

  • Access the Genomics England Research Environment HPC
  • Work with the available software to submit jobs to the different queues
  • Create and work with your own software on the HPC

Target audience

This training is aimed at researchers:

  • working with the Genomics England Research Environment
  • comfortable working on the command line
  • who can programme in python and/or R


12th December 2023, 1.30 pm


You can access the redacted slides and video below. All sensitive data has been censored.




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