Hands-on Next-Generation Sequencing Data Analysis

Aim

Workshop Objectives

Workshop Structure

📅 Day 1 – Introduction to NGS and Sequencing Data Fundamentals

• Introduction to Next-Generation Sequencing
• Evolution from Sanger sequencing to NGS
• Major sequencing platforms: Illumina, Ion Torrent, PacBio, and Oxford Nanopore
• Applications of NGS in genomics, transcriptomics, clinical research, agriculture, microbiology, and biotechnology
• Understanding raw sequencing reads
• Introduction to NGS file formats: FASTQ, FASTA, SAM, BAM, VCF, GTF/GFF
• Understanding Phred quality score, read length, depth, and coverage
• Overview of a standard NGS data analysis pipeline
• Difference between DNA-Seq, RNA-Seq, whole genome sequencing, targeted sequencing, and metagenomics

Hands-On Activity:

• Explore sample FASTQ files
• Identify read sequence and quality score information
• Prepare a basic NGS file format interpretation sheet

Hands-On Tools: Sample FASTQ Dataset, Google Colab / Linux Terminal Awareness, FASTQ Viewer, Google Sheets

📅 Day 2 – Quality Control, Read Cleaning and Preprocessing

• Importance of quality control in NGS data analysis
• Introduction to raw read quality assessment
• Understanding FastQC reports
• Per-base sequence quality, GC content, sequence duplication, and adapter contamination
• Introduction to MultiQC for combined QC reporting
• Why read trimming and filtering are required
• Adapter removal and low-quality base trimming
• Overview of tools such as FastQC, MultiQC, Trimmomatic, Cutadapt, and fastp
• Comparing raw reads and cleaned reads
• Preparing a QC summary for research reporting

Hands-On Activity:

• Run or review FastQC report on sample data
• Identify quality issues in sequencing reads
• Perform/read trimming demonstration using sample data
• Prepare a short QC interpretation note

Hands-On Tools: FastQC, MultiQC, fastp / Trimmomatic Awareness, Google Colab, Google Sheets

📅 Day 3 – Basic NGS Workflow Interpretation and Biological Reporting

• Overview of read alignment and reference genome mapping
• Introduction to aligners: BWA, Bowtie2, HISAT2, and STAR
• Understanding SAM/BAM files and mapping statistics
• Introduction to variant calling and VCF interpretation
• Introduction to RNA-Seq count data and gene expression analysis
• Basics of differential expression and biological interpretation
• Introduction to annotation and pathway interpretation
• Visualization of NGS outputs using basic plots and genome browsers
• How to prepare an NGS analysis summary report
• Common mistakes in NGS data interpretation

Hands-On Activity:

• Review sample alignment statistics
• Interpret a sample VCF or RNA-Seq count result
• Prepare a simple NGS interpretation summary table
• Draft a mini NGS data analysis report

Hands-On Tools: SAMtools Awareness, IGV Genome Browser Awareness, Excel / Google Sheets, Sample VCF / Count Matrix, Google Colab

Who Should Enrol?

Important Dates

Workshop Outcomes