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    Learn Ngs Variant Calling: A Hands-On Bioinformatics Course

    Posted By: ELK1nG
    Learn Ngs Variant Calling: A Hands-On Bioinformatics Course

    Learn Ngs Variant Calling: A Hands-On Bioinformatics Course
    Published 7/2025
    MP4 | Video: h264, 1920x1080 | Audio: AAC, 44.1 KHz
    Language: English | Size: 1.72 GB | Duration: 3h 24m

    Learn end-to-end variant calling using Linux and R: From Raw NGS data to variants with visualization and interpretation

    What you'll learn

    Understand the fundamentals of variant calling and its role in NGS data analysis.

    Set up a Linux environment for bioinformatics using Windows or native systems.

    Perform quality control and trimming of raw FASTQ sequencing data.

    Align sequencing reads to a reference genome using industry-standard tools.

    Use Samtools and FreeBayes to call SNPs and indels from aligned reads.

    Filter and refine variant calls to ensure accuracy and reliability.

    Visualize genomic variants using IGV (Integrative Genomics Viewer).

    Analyze and interpret VCF files using R and essential bioinformatics packages.

    Automate parts of the variant calling pipeline with shell scripting.

    Gain hands-on experience with real NGS datasets and submit results as assignments.

    Requirements

    No prior programming or bioinformatics experience is required — this course is beginner-friendly.

    A computer (Windows, macOS, or Linux) with at least 8GB RAM is recommended for smoother processing.

    Stable internet connection for downloading tools and datasets.

    Willingness to learn basic Linux commands (we’ll cover them step-by-step).

    Interest in genomics, DNA sequencing, or data analysis.

    Description

    Become a Variant Calling Pro Using Linux and R – No Prior Experience Needed!Unlock the secrets of the genome with hands-on training in variant calling! This course gives you practical skills to analyze next-generation sequencing (NGS) data using industry-standard tools like FreeBayes, Samtools, and R, all within a Linux environment. Whether you're a student, researcher, or clinician, this course empowers you to process FASTQ data, perform variant calling, visualize VCFs, and extract biological insights using open-source pipelines.What You'll Learn:Linux for Bioinformatics: Learn essential commands and file systems for data handling and tool usage.NGS Variant Calling Basics: Understand confidence, quality metrics, and key concepts in variant analysis.Pipeline Setup: Download datasets, prepare your analysis environment, and index genomes.Data Preprocessing: Run FastQC, trim reads, align with BWA, and prepare BAM files.Variant Calling with FreeBayes: Perform SNP and indel calling and filter low-quality variants.Visualization and Interpretation: View variants in IGV and interpret biological impact.R for Genomic Analysis: Set up R and use it to explore and visualize variant data.Assignments and Quizzes: Test your knowledge with assessments after each section.Who This Course Is For:Biology & Medical Students: Learn NGS data analysis without needing advanced programming.Researchers & Clinicians: Build reproducible pipelines for cancer genomics, rare diseases, and more.Bioinformatics Enthusiasts: Transition into genomics with a complete beginner-to-advanced course.Professionals in Biotech & Pharma: Strengthen your role in precision medicine and diagnostics.Course Features:Hands-on projects and real datasetsAssignments and quizzes after each sectionDownloadable scripts and guidesLifetime access and certificate of completionNo coding experience needed – just your interest in genomics and bioinformatics!

    Overview

    Section 1: Course Introduction

    Lecture 1 Introduction of Course

    Section 2: Basic Linux For Bioinformatics

    Lecture 2 Introduction to Linux

    Lecture 3 Environment Setup On Windows

    Lecture 4 Navigating The Linux File System

    Lecture 5 Basic Linux Commands For Bioinformatics

    Lecture 6 Working With Text Files And Data Processing In Linux For Bioinformatics

    Lecture 7 File Compression And Archiving In Bioinformatics

    Section 3: Introduction to Variant Calling

    Lecture 8 Introduction to Variant Calling in NGS Data

    Lecture 9 Understanding NGS Data Confidence for Variants

    Lecture 10 Variant Calling: Workflow and Key Activities

    Section 4: Preparing the Environment

    Lecture 11 Setting Up Tools and Environment for Analysis

    Lecture 12 Downloading Public NGS Data for Variant Calling

    Section 5: Data Preprocessing and Alignment

    Lecture 13 Quality Control and Trimming of Raw Sequencing Reads

    Lecture 14 Genome Indexing and Aligning Reads to Reference

    Section 6: Variant Calling and Filtering Using Freebayes

    Lecture 15 Using Samtools to Fix and Sort BAM Files

    Lecture 16 Calling and Filtering Variants from Aligned Reads

    Section 7: R and R Studio

    Lecture 17 Introduction of R

    Lecture 18 Setting Up R And R Studio For Bioinformatics

    Lecture 19 Package Installation In R

    Section 8: Variant Visualization and Interpretation

    Lecture 20 Visualizing and Interpreting Called Variants

    Biology and medical students who want to gain hands-on skills in next-generation sequencing (NGS) and variant analysis.,Researchers and lab professionals looking to analyze genomic data independently without relying on a bioinformatics team.,Beginner bioinformaticians who want to build their first variant calling pipeline using Linux and R.,Healthcare and biotech professionals seeking to understand variant data for clinical genomics, diagnostics, or personalized medicine.,Educators and instructors who want a complete, ready-to-teach variant calling workflow for academic or training purposes.,Anyone curious about how DNA variants are discovered, filtered, visualized, and interpreted from raw sequencing data.