Skip to main content

Getting started with the command line

The UNIX command-line interface (sometimes also called “command prompt” or “terminal”) is a way of interacting with the computer using only the keyboard. Many of the programs and tools used in bioinformatics are designed to work only from command-line, so it’s very important to get familiar with how the terminal works.

Although there are different types of terminals, all of them have an interface translating the text you type into meaningful commands that the computer can understand.

For this tutorial we’ll focus on the most commonly used command-line environment (or 'shell'), BASH (developed in 1989!), which is the default one for most Linux and MacOS systems. (It also works on Windows, but you have to manually install it.)

Why should we learn to use the command line?​

Here are some reasons:

  • For many tasks it’s faster than using a GUI (Graphic User Interface).
  • It's flexible: you can combine multiple programs, making the output of one the input of the next in a pipeline.
  • Most bioinformatics tools are made for the command-line.
  • It can efficiently handle big files that gui based tools might struggle to open.
  • The command line has lots of powerful commands for parsing text files.
  • High-performance computing: compute clusters don't usually have a GUI!
  • Some binary files (e.g. BAM or CRAM) can only be handled with dedicated command-line software (for example samtools).

To get started you need a terminal window -

When you're ready to start - go and start a terminal.