Course Overview
This comprehensive course provides an in-depth introduction to next-generation sequencing (NGS) and whole exome sequencing (WES), with a strong focus on variant calling. Designed for students, researchers, and early-career professionals, the course combines theoretical knowledge with hands-on practical training, enabling participants to process, analyze, and interpret genomic data using Linux-based bioinformatics tools. Participants will gain experience with the entire workflow, from raw data retrieval to functional analysis of identified variants.
Course Overview
The course begins with a detailed introduction to NGS and WES, covering sequencing technologies, platforms, and the advantages and limitations of these methods. Students will learn how to obtain raw exome datasets from any organism or disease context and understand the biological significance of haploid versus diploid organisms, germline versus somatic mutations, and the role of single nucleotide polymorphisms (SNPs), structural variations, and copy number variations (CNVs) in disease research.
Participants will then move on to hands-on training in quality control, trimming, and mapping of raw reads against reference genomes. The course introduces the Genome Analysis Toolkit (GATK) and Freebayes pipelines for variant calling, along with tools such as VCFtools, SnpSift, and SnpEff for variant filtration and annotation. Students will learn to identify SNPs, insertions/deletions (indels), structural variants, and CNVs, and predict the functional effects of variants to ensure accurate and biologically meaningful results.
The final section of the course focuses on downstream functional analysis. Students will gain experience in gene ontology (GO) analysis using topGO and enrichR, pathway analysis through KEGG, PANTHER, and Reactome, and data retrieval from major genomic repositories including ArrayExpress, Gene Expression Omnibus (GEO), and NCBI genome databases. Participants will also learn to handle genome assemblies, annotation files (GTF/GFF), and alignment files (SAM/BAM), providing a complete understanding of end-to-end NGS/WES analysis.
What You'll Learn
- • Fundamentals of NGS and whole exome sequencing
- • Retrieval of raw datasets and genome assemblies
- • Quality control, trimming, and mapping of raw reads
- • Variant calling using GATK and Freebayes
- • Filtering and annotation of SNPs, indels, CNVs, and structural variants
- • Variant effect prediction and functional interpretation
- • Gene ontology and pathway enrichment analysis
- • Hands-on experience with Linux-based command-line bioinformatics tools
Who Should Enroll
This course is ideal for students, graduates, and researchers in Biotechnology, Bioinformatics, Molecular Biology, Genetics, and related life sciences who wish to gain practical skills in NGS/WES analysis and variant interpretation for research or industry applications.
