Using the command line

Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

A lot of genomics analysis is done using command-line tools for three reasons:

Getting Started

This lesson assumes no prior experience with the tools covered in the module. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population.

Participants should bring their laptops and plan to participate actively.

This lesson uses an Amazon Machine Instance (AMI). If you are attending a tutor-led workshop your AMI will be created for you and will be sent the log in information you will need for this lesson. If you are self-studying Prenomics, you will need to set up your own instance using our Create Your Own AWS Instance module.

Before starting this lesson, you should go through the Files and Directories lesson.


00:00 1. Navigating Files and Directories How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient?
00:50 2. Working with Files and Directories How can I view and search file contents?
How can I create, copy and delete files and directories?
How can I repeat recently used commands?
01:35 3. Redirection How can I search within files?
How can I combine existing commands to do new things?
02:20 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.