Master The Command Line: From Fastq To Vcf For Ngs Analysis

Analyze real NGS data from FASTQ to VCF using command-line tools - fully compatible with Linux, WSL, and Windows users

What you'll learn

Download and extract raw sequencing data from the NCBI Short Read Archive using command-line tools

Assess and improve the quality of FASTQ files using FastQC and fastp

Align sequencing reads to a reference genome with BWA, and process SAM/BAM files using samtools

Call and filter genomic variants (VCF) using bcftools, and understand how to interpret the results

Organize NGS analysis projects in a clean directory structure for reproducibility and clarity

Understand the structure of FASTQ, SAM, and VCF files and extract meaningful information from each format

Use standard Linux command-line tools to manipulate large genomic files efficiently

Requirements

No prior experience with bioinformatics is required

Basic familiarity with the Linux terminal is helpful, but not mandatory — key commands are explained step by step

An internet connection is required to download sequencing data and reference files

A computer with at least 4 GB RAM is recommended for smoother performance during alignment and variant calling

Description

This course is a complete hands-on guide to processing real next-generation sequencing (NGS) data from raw FASTQ files to final VCF variant calls - all using command-line tools in a Linux environment.You will learn to install and use essential bioinformatics tools such as fastqc, fastp, bwa, samtools, and bcftools. These tools are the foundation of most modern NGS pipelines used in genomics research. If you're a Windows user, no problem - we’ll show you how to set up WSL (Windows Subsystem for Linux), so you can follow every step directly from your own machine.The course is structured around short, focused lessons. Each one walks you through a specific task in the sequencing data pipeline: downloading data from NCBI’s SRA, performing quality control checks, trimming low-quality reads and adapters, aligning reads to a reference genome, processing alignment files, and calling SNPs and indels to generate clean, filtered VCF files.This course is ideal for beginners and intermediate users alike - whether you’re a student, researcher, or bioinformatics enthusiast. You don’t need any prior experience with Linux or the command line. By the end of the course, you’ll have a complete working pipeline and the confidence to analyze real NGS datasets on your own.

Overview

Section 1: Setup and Installation

Lecture 1 (optional) For Windows Users - Installing WSL

Lecture 2 Command Line Tools Installation

Section 2: Downloading and Preparing FASTQ Files

Lecture 3 SRA to FASTQ

Lecture 4 Checking FASTQ Read Quality with FastQC

Lecture 5 FASTQ Trimming and Quality Filtering

Section 3: Read Alignment and SAM/BAM Processing

Lecture 6 Reference Genome Indexing

Lecture 7 Read Alignment with BWA

Lecture 8 Inspecting SAM Files

Lecture 9 Processing Alignments with Samtools

Section 4: Variant Calling and VCF Interpretation

Lecture 10 Variant Calling with bcftools

Lecture 11 Understanding the VCF Format

Students, researchers, and lab technicians who want to learn how to analyze NGS data from FASTQ to VCF using command-line tools,Biologists and geneticists with no programming background who need a practical, step-by-step introduction to genomic data analysis,Bioinformatics beginners looking to understand how tools like fastqc, fastp, bwa, samtools, and bcftools work together in a complete pipeline,Anyone who wants to build a reproducible and efficient workflow for variant calling using only free and open-source tools