What Is Linux and the Command Line?

What Linux Actually Is

Linux is an operating system, the master program that controls a computer's hardware and runs all of your other software, just as Windows or macOS does. At the center of Linux sits the kernel, the core piece of code that talks directly to the processor, memory, and storage on your behalf. Most scientific computers, web servers, and supercomputers run Linux because it is free, open, stable, and can be driven entirely through typed text commands.

Terminal, Shell, and Bash

The terminal is simply a window that displays text and lets you type instructions to the computer instead of clicking buttons. The shell is the program running inside that window that reads what you type, carries it out, and prints the result back to you. The most common shell on Linux is called bash, while modern macOS ships with a very similar shell called zsh. For the simple commands in this course the two behave the same, so when a tutorial says to run something in the shell you can type it into either one.

Why Bioinformatics Lives Here

Modern sequencing machines produce data files that are many gigabytes in size, and these usually live on remote high-performance computing clusters, commonly called HPC clusters, that you reach across a network with no desktop or mouse. Almost every core bioinformatics tool, from read aligners to variant callers, is distributed as a command-line program with no graphical interface. Because each typed command can be saved as text and run again exactly, the command line is also the foundation of reproducible science.

Anatomy of a Command

ls -lh /data/reads

When the shell is ready it shows a prompt, usually a short line ending in a dollar sign, and you type your command right after it. A command has three parts, visible in ls -lh /data/reads: the command name ls that lists files, the options -lh that adjust how it behaves (l for a detailed long listing, h for human-readable file sizes such as 4.0K or 2.3G), and the argument /data/reads that names the folder to act on. Options normally begin with a dash and each part is separated by a space, a pattern you will meet in nearly every tool you run.

whoami
date
echo "Hello, Linux"

sudipta
Mon Jul 13 09:20:14 UTC 2026
Hello, Linux