Module 1: Linux for Bioinformatics

This module introduces the Linux command line for bioinformatics workflows. You will learn how to navigate files, inspect sequencing data, and use core Unix tools that are standard in bioinformatics pipelines.

Linux is essential in bioinformatics because most tools run on the command line and expect a Unix-like environment. Understanding Linux basics lets you work efficiently on local machines and remote servers.

Learning objectives

By the end of this module, you will be able to:

• Navigate directories and manage files using core commands
• Inspect and summarize text-based bioinformatics files
• Use pipes and redirection to build small workflows
• Write simple scripts and manage permissions
• Connect to remote systems with SSH and move files with SCP

Lessons

• Lesson 1: Fundamentals and basic commands
  • Covers navigation, file listing, and basic file operations
• Lesson 2: Text processing, pipes, and redirection
  • Introduces grep, sort, uniq, and combining commands with pipes
• Lesson 3: Scripting and permissions
  • Explains executable scripts, permissions, and safe automation
• Lesson 4: SSH and remote work
  • Shows how to connect to remote systems and transfer files
• Lesson 5: Absolute and Relative Paths
  • Covers the root directory, absolute vs. relative paths, and navigating mounted drives (/mnt)

Note: All examples and exercises use the data in Training/.