BIO HELP LEARNING COURSE

Linux and Command Line for Bioinformatics

Learn the Linux command line the way bioinformaticians use it: navigate servers, handle huge sequencing files, write shell scripts and manage software with Conda.

Programming

◉ Beginner◷ 10 Hours▣ Certificate Included

Course Information

Everything you need to know before enrolling.

LANGUAGEEnglish

Pre-Register for Live Training

Registration for the next live batch opens soon. Pre-register and our team will contact you with the batch dates, fees and registration link as soon as it opens.

Live online classes
Group & college batches
Certificate on completion

Pre-register for live training → Ask on WhatsApp Or email [email protected]

▤ Overview ☷ Curriculum ♙ Instructor ☆ Reviews ▣ FAQs

▤

About This Course

Almost every bioinformatics tool runs on Linux, usually from the command line on a remote server. This course removes the fear of the black terminal window and makes you productive in it.

You learn to move around the file system, inspect and search FASTA and FASTQ files, chain commands with pipes, automate tasks with shell scripts, install tools with Conda and work on a remote machine over SSH.

Who this course is for

Life-science students who have never used a terminal
Researchers starting NGS or genomics analysis
Learners preparing for any NGS course at Bio Help Learning

Prerequisites

No prerequisites. Basic computer use is enough.

Final project

Organize a raw sequencing project folder and write a shell script that summarizes every FASTQ file in it.

◎

What You’ll Learn

✓Navigate the Linux file system confidently

✓Inspect, search and count records in FASTA and FASTQ files

✓Combine commands with pipes and redirection

✓Use grep, awk, sed, sort and uniq on biological data

✓Write and run reusable shell scripts

✓Install and manage tools with Conda environments

✓Connect to and work on a remote server

⌘

Tools & Technologies

Linux (Ubuntu)WSLBashgrepawksedCondaSSHnanoFastQC

Course Curriculum

What you will learn, module by module

8 modules 10 hours of training 32 topics Certificate on completion

- Linux, servers and the command line
- Installing Ubuntu or WSL on your computer
- Opening the terminal and running your first commands
- Getting help with man and --help
- Absolute and relative paths
- pwd, ls, cd, mkdir, cp, mv and rm
- Wildcards and tab completion
- Organizing a bioinformatics project folder
- cat, less, head and tail
- Reading FASTA and FASTQ structure
- Working with compressed files (gzip, zcat)
- Counting lines and reads with wc
- Pattern search with grep
- Regular expressions basics
- Counting sequences and extracting headers
- Finding motifs in sequence files
- Pipes and output redirection
- cut, sort, uniq and tr
- Column processing with awk
- Find and replace with sed
- File permissions and chmod
- Running jobs in the background
- Monitoring with top and htop
- Checking disk usage with du and df
- Writing and running a Bash script
- Variables, loops and conditions
- Looping over many sample files
- Making scripts reusable with arguments
- Installing tools in Conda environments
- Connecting with SSH and copying files with scp
- Running FastQC from the command line
- Mini project: summarize a FASTQ folder with a script

♙

Your Instructor

Bio Help Learning Educator

Bioinformatics Educator & Mentor

Learn from experienced educators and practitioners through practical, career-focused bioinformatics training.

Frequently Asked Questions

6 answers about this course

Do I need any programming experience?

No. The course starts from opening the terminal and builds up step by step.

Can I do this course on Windows?

Yes. We show how to install WSL so you can run Linux inside Windows.

Which course should I take next?

Introduction to NGS and Sequencing QC, which uses the Linux skills from this course.

Will I get a certificate?

Yes, after completing all modules, the quizzes and the final project.

How do I get fee and batch details?

Pre-register on this page or contact us on WhatsApp, and our team will share the details.

How long will I have access to the course?

You get full access to all course materials for 3 months from the date of enrollment.

Still have a question?Our team usually replies within one working day.

Ask on WhatsApp →

WHAT OUR LEARNERS SAY

Real Stories. Real Growth.

Hear from learners building practical skills with Bio Help Learning.

★★★★☆

I really enjoyed the course and found it very useful: it gave a clear and practical overview of the whole WGS workflow, from raw reads to a VCF, and the hands-on sessions helped a lot.

Marc Peralta SerranoUniversity of BarcelonaWhole Genome Sequencing (WGS) Data Analysis Training

★★★★★

The workshop provided me an understanding of the principles and techniques involved in bioinformatics, molecular docking, protein-ligand interactions, homology modeling, and drug design.

Ridam BhowmickMaulana Abul Kalam Azad University of Technology, West Bengal.Molecular Docking and Drug Discovery

★★★★★

As i am from biotechnology background this workshop, actually very helpfull for me

Anushka ChavanDeogiri college AurangabadBioinformatics Training

★★★★★

Learn about different molecular docking tools.

Shovan NaskarIndian Institute of Technology (Banaras Hindu University), VaranasiBioinformatics Workshop

★★★★★

This workshop helped me to learn working with various softwares and also to develop an interest over drug designing

Subhodeep SahaUniversity of CalcuttaBioinformatics Training

★★★★★

From this workshop I learned many new things such as docking, about new websites,how to use Swiss software,basic bioinformatics etc, it's very helpful for me.

Sayan DuttaUniversity of CalcuttaBioinformatics Training

★★★★☆

The workshop was informative and provided valuable insights into bioinformatics tools and techniques.

Santhosh M EReva University BangaloreBioinformatics Tools and Techniques

★★★★★

The Drug Discovery Workshop was highly informative and helped me gain valuable knowledge about the drug discovery process, including molecular docking, drug–target interactions, and computational tools used in drug design.

ANUSHA P VCSIR-CCMB, Hyderabad IndiaDrug Discovery Workshop

View More Reviews →

OUR GLOBAL LEARNERS