Quick Unix/Linux command line shell

The key to power bioinformatics

The command line shell is the main way to interact with most powerful computing systems and bioinformatics tools. This course provides what you need to get going with the shell.

Next session: October 2020


  • Matthew Hartley
  • Burkhard Steuernagel


For those new to the command line shell with a need to use it.


Many bioinformatics applications and pipelines require knowledge of the unix command line shell. In particular, High Performance Computing (HPC) systems work with a command line interface. In addition, the shell provides a powerful tool for saving time and making computational work reproducible. This course is intended for those with no previous experience of the command line shell, and aims to enable attendees to use command line applications.


9:30 Start
11:00 Coffee break
13:00 End

Learning outcomes

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



Full course syllabus

Course materials

Course book