Day 1: Introduction to NGS and Sequencing Data Fundamentals
Focus:
This session introduces participants to the fundamentals of Next-Generation Sequencing, sequencing platforms, raw sequencing reads, common file formats, and the basic structure of an NGS data analysis pipeline.
Topics Covered:
- 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
Focus:
This session focuses on quality assessment of raw sequencing reads, interpretation of FastQC reports, read trimming, adapter removal, and preparation of cleaned reads for downstream analysis.
Topics Covered:
- 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
Day 3: Basic NGS Workflow Interpretation and Biological Reporting
Focus:
This session introduces participants to basic downstream NGS workflow interpretation, including read alignment, mapping statistics, variant interpretation, RNA-Seq count data, differential expression awareness, visualization, and biological reporting.
Topics Covered:
- 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
