Command-line tools for genomics

We continue with an introduction to Command-Line. This module takes an estimated 2 hours to complete.

What Is Command-line?

The command-line, also called command screen, or text interface is a user interface that's navigated by typing commands at prompts, instead of using a mouse.

Why Should I Learn Command-Line?

Using a command-line, you can perform almost all the same tasks that can be done with a GUI, but quicker and easier to automate and do remotely. Good knowledge of the command-line is an essential skill for any successful bioinformatician, as most of the common bioinformatics tools operate in the command-line environment.

What Are The Learning Outcomes of the Week?

At the end of this week, you should:

  • Know how to connect to the server and use the command-line

  • Be familiar with the Bash terminal & the Linux command-line

  • Get familiar with sequencing and annotation file formats

  • Get familiar with common command-line tools for genomics

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