Single Nucleotide Polymorphism (SNP) Detection and Analysis using NGS
“Precision Genomics: Decoding SNPs for a Healthier Future”
The Single Nucleotide Polymorphism (SNP) Detection and Analysis workshop using Next-Generation Sequencing (NGS) is an intensive program designed to equip participants with comprehensive knowledge and practical skills in identifying, analyzing, and interpreting SNP data through NGS technology. The workshop typically covers fundamental concepts of SNP variation, NGS data generation, preprocessing, and quality control steps, as well as diverse SNP calling methodologies. Participants engage in hands-on sessions, leveraging bioinformatics tools and software for SNP analysis, validation methods, and data interpretation. Additionally, the workshop explores the practical applications of SNP analysis in diverse fields like medical genetics, evolutionary biology, and personalized medicine while discussing emerging trends and challenges in SNP detection and analysis. Ultimately, it aims to empower researchers, students, and professionals with the necessary expertise to effectively utilize NGS data for SNP identification and interpretation in various genetic studies and applications.
Aim: The aim of this workshop is to equip participants with a deep understanding of single nucleotide polymorphism (SNP) analysis through the application of Next-Generation Sequencing (NGS) techniques. By the end of the workshop, participants will possess the knowledge and practical skills necessary to perform accurate and meaningful SNP analysis.
What you will learn?
- Introduction to NGS Technology
- Overview of NGS data formats
- Accessing NGS data using SRA tool kit
- Checking sequence quality using FastQC
- Cleaning the sequences using cutadapt
- Aligning sequences using BWA
- Sorting the BAM alignment files
- Mark PCR duplicates in BAM alignment files using Picard
- Use FreeBayes and Delly on the BAM files to identify variants (SNPs and indels)
- Visually inspect read mapping and variant calls with the Integrated Genomics Viewer (IGV)
Note: Linux OS is required for running the tools
Intended For : Graduates, Post Graduates, Research Scholars, Academicians, Industry Professionals of Biology, Genetics, Bioinformatics, Pharmaceutical and Biotech companies.
Career Supporting Skills
- Demonstrate Proficiency: Understand the fundamental concepts of SNP analysis using NGS and demonstrate proficiency in applying these concepts to real data.
- Perform SNP Detection: Confidently perform SNP detection and annotation using NGS data, including the ability to differentiate between true variants and sequencing errors.
- Interpret Genetic Variants: Interpret the biological and clinical significance of detected SNPs, including their potential impact on genes and gene products.
- Utilize Bioinformatics Tools: Use bioinformatics tools and software for SNP analysis and related bioinformatics tasks.
- Apply Population Genetics: Apply SNP analysis techniques in the context of population genetics, including assessing genetic diversity and conducting association studies.
- Quality Assurance: Implement best practices for quality control and quality assurance in SNP analysis, ensuring the reliability and reproducibility of results.
- Research Readiness: Be prepared to apply the knowledge and skills gained in the workshop to their own research projects or work in genetics, genomics, or related fields.
- Critical Analysis: Critically analyze and interpret SNP data, understanding its implications for genetic research, personalized medicine, and disease studies.