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 course. 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 is part of a course that uses data hosted on an Amazon Machine Instance (AMI). Course participants will be given information on how to log-in to the AMI during the course. Information on preparing for the course is provided on the Cloud-SPAN Genomics Course setup page.


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.