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Getting started with the command line

Welcome! The UNIX command-line interface (sometimes also called “command prompt” or “terminal”) is a way of interacting with the computer using only the keyboard. If you haven't seen one before, it looks something like this:

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Many of the programs and tools used in bioinformatics are designed to work only from command-line, so for genomic analysis it’s very important to get familiar with how the terminal works.

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.