Linux for Bioinformatics: Beginner to Advanced

Name: Linux for Bioinformatics: Beginner to Advanced
Rating: 4.6 (93 reviews)

Learn Linux commands, shell scripting, file systems, pipelines, and essential tools for bioinformatics workflows.

Highest Rated

Created bySara Youssef

Last updated 6/2026

English

What you'll learn

Gain a deep understanding of Linux and its significance in the field of biology.
Master the structure of a Linux file system and navigate it effortlessly.
Utilize powerful Linux commands to manipulate and analyze biological data files.
Acquire the ability to write and execute shell scripts to automate data processing tasks.

Course content

5 sections • 43 lectures • 5h 46m total length

What is Linux?3:20
What is Virtual Machine?1:44
Linux distributions2:57
How can I install VM?3:53
Ubuntu Installation and How to Create Your Virtual Machine7:31

What is terminal and why we use it? Here is our first command!8:32
mkdir, cat15:42
pwd, cd16:19
Moving between directories15:11
Quiz 1
ls Command and The Concept of Wildcard9:57
Learn how to list directory contents with ls, using -l, -h, and -a for permissions, ownership, human-readable sizes, and hidden files, plus wildcards to match patterns.
Files Permissions (chmod)10:58
Learn how to set Linux permissions for files and directories using chmod, assign read, write, and execute rights to owner, group, and others, and verify with ls -l.
Files Permissions using Numeric Mode5:23
rm Command6:44
mv Command8:51
cp Command5:22
Linux Command Practice Assignment-1

What is Shell and Bash?5:52
Explore the shell and Bash on Linux, and learn to interact with the OS via the command line, automate tasks with Bash scripting, and use variables, loops, conditionals, and functions.
Our First Script Using 'for' Loop!20:10
What is The Variable?3:06
Understand how a variable stores values in bash, using the file name variable in a for loop to substitute names like basilisk, spyridium, and unicorn in commands.
Vim Text Editor7:58
Case-110:55
Learn to write bash scripts with interactive prompts, using echo and read to store user input in variables and print personalized greetings in case one.
Case-29:04
Nano Text Editor6:29
Case-3 - if Statement Part-17:20
Case-4 - if Statement Part-211:44
Case-5 - if Statement in Bioinformatics6:20
What is 'for' Loop? Example: 112:26
Showcases bash for loops to iterate over fasta files, extract and sort header lines, remove duplicates, and write sorted headers to files named after the originals with headers to text.
'for' Loop in Bioinformatics - Example: 28:57
What is 'while' Loop? Example: 17:41
'while' Loop in Bioinformatics - Example: 25:34
Calculating GC Content of DNA Sequences Using a Bash Script2:30
'while' Loop in Bioinformatics - Example: 38:17
A Message to my Dedicated Students!4:43
Assignment: 3
Assignment: 4
Assignment: 5

Requirements

No prior knowledge of computing or bioinformatics is expected. There are no formal prerequisites.

Description

Linux is one of the most important skills in modern bioinformatics and computational biology. Many bioinformatics tools, pipelines, and sequencing workflows are designed to run in Linux environments, making Linux knowledge essential for researchers, students, and professionals working with biological data.

This beginner-friendly course will teach you the Linux fundamentals required for bioinformatics analysis and data processing.

You will learn how to:

Navigate the Linux command line confidently
Work with files and directories efficiently
Understand Linux file systems and permissions
Manipulate biological data files using Linux commands
Prepare data for downstream bioinformatics analysis
Write and execute Bash scripts
Automate repetitive data processing tasks
Work with real biological datasets in practical scenarios

Throughout the course, you will gain hands-on experience using Linux tools commonly applied in bioinformatics workflows and computational biology environments.

No prior Linux experience is required. The course is designed for beginners who want to build practical Linux skills for research, genomics, sequencing analysis, and bioinformatics applications.

What You Will Learn

Linux Fundamentals

Linux operating system basics
Terminal and command-line navigation
File and directory management

Working with Biological Data

Handling sequence and biological data files
Searching, filtering, and processing data
Data preparation for analysis pipelines

Bash Scripting

Writing simple Bash scripts
Automating workflows
Improving productivity and reproducibility

Practical Bioinformatics Applications

Real-world examples using biological datasets
Linux tools used in bioinformatics environments
Best practices for computational workflows

By the end of this course, you will have a solid foundation in Linux and the practical skills needed to work more efficiently in bioinformatics and computational biology projects.

Enroll today and start building one of the most valuable skills in bioinformatics.

Who this course is for:

This course will appeal to students, biologists, and research scientists with an interest in bioinformatics.
Interest in bioinformatics
Willingness to learn.
Basic knowledge of biology (preferred, but not mandatory).

Linux for Bioinformatics: Beginner to Advanced

What you'll learn

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Course content

Introduction5 lectures • 19min

Fundamentals10 lectures • 1hr 43min

Our First Real Tutorial6 lectures • 54min

Let's Start our Bash Scripting!17 lectures • 2hr 19min

Sequence Alignment Using GUI & CLI5 lectures • 31min

Requirements

Description

Who this course is for: