> For the complete documentation index, see [llms.txt](https://edu.abi.am/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://edu.abi.am/ngs-data-analysis-and-functional-genomics/the-linux-command-line.md).

# The Linux Command-line

## 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.

## Learning outcomes

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