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:
- you will often be working with a large number of files, and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks,
- you will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface, and
- you will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if in fact a GUI tool even exists).
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.