NGS Data Analysis

This course equips participants with upstream analysis knowledge and practical skills for NGS data, covering Bash scripting, quality control, metagenomics, transcriptomics, variant analysis, single-cell sequencing, and multi-omics integration. Course abbreviation: NGS Instructor: Mohamed Emam PhD student/researcher at Bioinformatics and Evolutionary Genomics Group, University of Porto, Portugal. Workload: 12 lectures, 3 hours each. Total workload: 42 hours: 36 hours of lectures and tutorials and 6 hours of self studies. Entrance requirements: Basic knowledge of biology and computer science. Used media: PowerPoint presentation

Objectives

• Understand Next-Generation Sequencing technologies and platforms
• Process and prepare raw sequencing data for downstream analysis
• Use Bash scripting for upstream analysis workflows
• Analyze NGS data quality, filtering, alignment, and pseudo-alignment
• Explore microbiome workflows and variant analysis basics

Competences to be Developed

• Bash scripting and command-line workflows
• NGS data quality checking and filtering
• Alignment and pseudo-alignment algorithms
• Microbiome analysis using EBI workflows, taxonomic assignment, diversity analysis, and visualization
• Variant analysis using SAMtools and GATK
• Research project development and scientific discussion

Assessment

• Finalize a research project applying learned methods
• Present, discuss, and scientifically review projects in the last lecture

Assessment and completion

• Quizzes: 20%
• Assessments: 30%
• Final / Graduation Project: 50%
• Overall passing grade: 60%
• Minimum project grade: 50%
• All mandatory components must be completed
• One reassessment or resubmission opportunity is available for a failed mandatory assessment or final project