Introduction to the Command Line for Bioinformatics

26 June 2023 to 26 June 2023 - 09:30-16:30
The Diamond - Workroom 2
Mark Dunning

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This workshop is for University of Sheffield researchers. Please ensure that you sign up using a University of Sheffield email address so that your booking is accepted.

This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We give example of processing data arising from Next-Generation Sequencing experiments, in particular an RNA-seq experiment. However, the tools presented should be applicable to other types of high-throughput biological data.


No prior programming experience is required. You will need to bring your own laptop to the session, but there is no software to install. Some familiarity with the experimental techniques used in Next-Generation Sequencing experiments would be advantageous.

Learning Outcomes

After this course you should be able to:

  • Connect to a Unix / Linux system
  • Navigate around a file system by issuing commands; rather than using a Desktop environment
  • Move and copy files and directories within the Linux system
  • Work with text files
  • Run programs from the command-line
  • Configure a pipeline using the nextflow workflow manager


During this course you will learn about:

  • Interacting with a Linux system using a command-line interface
  • A best-practice workflow for RNA-seq analysis
  • The importance of reproducible analysis pipelines
  • The nextflow system as an example of a workflow manager

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