Bioinformatics: Learn NGS Data Analysis From Scratch

Name: Bioinformatics: Learn NGS Data Analysis From Scratch
Rating: 4.5 (255 reviews)

Best Bioinformatics course to Learn Bioinformatics NGS Variant Calling Data Analysis from Scratch (Theory & Practical)

Created byNaeem Mahmood Ashraf

Last updated 6/2025

English

What you'll learn

You will learn the fundamentals of Molecular Biology From Genotype to Phenotype
You will installation of Linux in Windows (WSL) and fundamentals of bash scripting
You will learn about the FASTQ and FASTA file formats
You will learn the installation of tools for Variant Calling in Linux
You will learn the GATK best practice pipeline for Variant calling starting from FASTQ to VCF
You will learn the structure of VCF file and understanding of its information
You will learn about Annotations of Variants present in FASTQ file using Funcotator
You will learn the sorting of Annotated VCF file to take clinical decisions
You will learn how to leverage the open source software to analyze the NGS data

Course content

6 sections • 68 lectures • 4h 21m total length

Important Instructions1:48
Join this bioinformatics course to master NGS data analysis from scratch by completing 66 tutorials, using downloadable PDFs and command guides for practicals, and tackling assignments with expert Q&A support.

What is DNA?3:13
Where DNA is present?1:59
Why DNA is So Important for Life?1:46
Genotype and Phenotype?2:09
What Genes Have?2:17
Difference Between Eukaryotic and Prokaryotic Genes2:55
Mutations; Raw Material of Evolution3:07
Different types of Mutations4:50
Different types of Large Chromosomal Changes1:49
Difference Between Germline and Somatic Mutations1:48
What are SNPs?2:03
Quiz-1: Test Your Knowledge of Molecular Biology

What is Sanger Sequencing?2:19
Limitation of Sanger Sequencing3:55
Practical-2.1: Analysis of Sanger Sequencing Quality5:02
Assignment-1: Please Check the Quality of Sanger Sequencing AB1 File
Next Generation Sequencing (NGS) Fundamental Methodology2:06
What is FASTQ File?2:41
Understanding the Quality Scores2:54
Concept of Paired End and Single End Sequencing Data2:21
NGS Data Analysis Workflow2:47
Quiz-2: Test Your Knowledge of Sequencing Technologies

Fundamentals of Computer Hardware & Operating Systems4:53
Practical 3.1: Installation of Linux Operating System (Part-1)1:13
Discover how to install the Linux operating system for ngs data analysis, including options for Windows users and guidance on using Mac terminals.
Practical-3.2: Installation of Ubuntu in Windows (WSL)3:27
Practical-3.3: Some Fundamental Commands to Navigate in Linux System5:58
Magical Words to Install Tools in Linux2:37
Practical-3.4: Installation of FASTQC, BWA & Samtools4:56
Practical-3.5: Installation of Hisat21:29
Practical-3.6: Trimmomatic Tool (Downloading and Use)2:58
Practical-3.7: GATK Donwloading and Setting Path7:00
Practical-3.8: Quality Checking of FASTQ File Using FASTQC4:39
Understanding the Output of FASTQC Report12:15
Assignment-2: Analyze the Quality of Reads In FASTQ File Using FASTQC Tool
Practical-3.9: Trimming of FASTQ File5:43
Fundamentals of Alignment; Basic Concept3:41
Some Common Aligners Available2:58
Practical-3.10: Increasing the Swap Memory in Ubuntu4:52
Assignment-3: Increase Your SWAP Memory (Optional)
SAM & BAM Files That You Will Have After Alignment; Basic Introduction1:20
Practical-3.11: How to Get the Reference Genome For HISAT23:44
Practial-3.12: How to Build Reference Genome For HISAT25:48
What Is Read Group and Its Importance in GATK2:37
Pratical-3.13: How to Get the Read Group From FASTQ File2:01
Assignment-4: Get an Idea About Read Group Info
Practical-3.14: Alignment Using Hisat2 (Method-1)6:52
Assignment-5: Build SAM File Using Hisat2
Downloading Reference Genome For BWA and GATK2:07
Practical-3.15: Making Index File for BWA3:43
Practical-3.16: Alignment Using BWA (Method-2)3:22
Practical-3:17:Conversion of SAM file to BAM file6:21
Assignmnet-6: SAM to BAM File Conversion
Understanding of Marking Duplicates in BAM File1:46
Practical-3.18: Marking the Duplicates in the BAM File2:14
Assignment-7: Lets Mark the Duplicates in the BAM File
Base Quality Sequence Recalibration (BQSR) Concept5:05
Practical-3:19: Making Index Files For GATK Pipeline3:52
Assignment-8: Lets Create Some Important Files for GATK Pipeline
Practical-3.20: Applying BQSR (Base Recalibration)5:06
Assignment-9: Lets Recalibrate the Base Quality Scores
Understanding of HaplotypeCaller of GATK1:50
Practical-3:21: Building VCF File Using Haplotype Caller of GATK3:21
Assignment-10: Lets Finally Build the VCF File
Quiz-3 Test Your Knowledge About FASTQ to VCF Conversion

Inspection of VCF File in Text Editor and Excel5:09
Assignmnet-11: Lets Inspect the VCF File
Practical-4.1:Getting rsIDs of Varients4:28
Assignment-12: Lets Starting Annotating the VCF File
Practical-4.2: Sorting SNPs and Indel's4:34
Assignment-13: Lets Separate the SNPs & Indels from VCF File
Structure of the VCF File, MetaData and Record Table5:14
Getting Idea About Genotype8:40
Concept of Allelic Depth and Total Depth2:28
Concept of Genotype Quality and Likehood of Genotype3:16
Practical-4.3: Sorting of Variants in Excel4:19
Quiz-4: Test Your Knowledge About VCF File

What is Funcotator?6:19
A Database Needed By Funcotator5:20
Practical -5.1: Performing Annotation Using Funcotator7:09
Understanding the Output of Funcotator3:13
Assignment-14: Lets Add Functional Annotations in Our VCF
Demonstration of VCF File Created Using Gnom_AD3:16
Practical-5.2: Easy Sorting of VCF File Into TSV File4:53
Learn to sort an annotated vcf file into a tidy tsv with a Python script on Ubuntu, producing a human readable, tab separated file for easy sorting in Excel.
Assignment-15: Lets Explore the Annotated Clean File
Demonstration of VCF File Created Using Somatic DataSources6:27
Sorting of Variants For Cancer2:47
Assignment-15: Lets Explore the VCF File that is Annotated Using Somatic Dataset
Quiz-5: Test Your Knowledge About Funcotator

Requirements

No prior knowledge of programming is needed.
Fundamental knowledge of Molecular Biology is needed but not mandatory. You will learn some essential molecular biology knowledge in first module of course.
Fundamentals of Bioinformatics is needed but not mandatory. You will learn most of its part related to NGS data analysis in course
In online teaching, it's always hard to engage the students. Therefore we have designed this course keeping the psychology of students in view. Usually, students start to lose their interest when they are stuck in a complex concept that's why We tried to move from simple to complex easily and understandably.

Description

Become a Bioinformatics Pro with Hands-On NGS Data Analysis Skills!

Next-Generation Sequencing (NGS) is transforming healthcare, research, and biotechnology. With bioinformatics expertise now essential for biologists, clinicians, and researchers, this Udemy course empowers you to analyse human genomic data like a pro using the GATK pipeline (Genome Analysis Toolkit). Master industry-standard workflows to process FASTQ files, call variants, annotate VCFs, and unlock insights for personalised medicine, cancer genomics, and rare disease research.

Why This Course?

Ranked #1 Skill in Genomics: Bioinformatics is critical for interpreting NGS data. Stand out in academia, pharma, or clinical labs.
Zero to Pipeline Mastery: No prior coding experience needed! Learn end-to-end NGS analysis for human genomes (WGS/WES).
GATK-Certified Workflows: Follow best practices endorsed by the Broad Institute for accurate, reproducible results.
Career-Ready Projects: Analyse real datasets, annotate variants with Funcotator, and build a portfolio for job applications.

5 Modules to Master NGS Bioinformatics:
Bioinformatics Basics for Biologists: DNA, RNA, genomic variations, and sequencing fundamentals.
NGS Technologies & Data Generation: Illumina, and data formats (FASTQ, BAM, VCF).
GATK Pipeline: FASTQ → BAM → VCF: Quality control, alignment (BWA), duplicate removal, and variant calling.
VCF File Mastery: Interpret variants, filter low-quality calls, and prioritise clinically relevant mutations.
Funcotator for VCF Annotation: Predict functional impacts (pathogenic vs. benign) and generate clinical reports.

Who Should Enrol?

Biologists & Clinicians: Analyse genomic data without relying on bioinformaticians.
Researchers: Publish robust findings using reproducible NGS workflows.
Students: Boost employability with in-demand bioinformatics skills.
Biotech Professionals: Upskill for roles in precision medicine, oncology, or diagnostics.

What’s Included?
Downloadable Workflows: Automate analysis with ready-to-use scripts.
Practice Datasets: Human genomic data
Certificate of Completion: Showcase your skills on LinkedIn/resumes.
Lifetime Access: Stay updated with NGS advancements.

Disclaimer: Focused on human genomic data (WGS/WES). Microbial workflows differ and are not covered.

Who this course is for:

Beginner in field of Biology
Beginners in field of Bioinformatics
Beginners in molecular diagnostics
Data scientists interested to understand genomic (DNA) data
Researcher pursing their carrier in Molecular biology, Biochemistry and Biotechnology

Bioinformatics: Learn NGS Data Analysis From Scratch

What you'll learn

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Course content

Some Important Words Before Start of the Course1 lecture • 2min

Fundamentals of Molecular Biology11 lectures • 28min

Introduction of Sequencing Technologies (Foucs on NGS)8 lectures • 24min

NGS Data Analysis From FASTQ to VCF32 lectures • 2hr 10min

Understanding of VCF File8 lectures • 38min

Annotation of VCF File Using Functotator8 lectures • 39min

Requirements

Description

Who this course is for: