NGS Data Analysis

About Course

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

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
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

Course Content

Lecture 1: Introduction to NGS Technologies and Platforms

Introduction to NGS Technologies and Platforms

00:00

Lecture 2: Introduction to Bash

Lecture 3: NGS Topics – Metagenomics Part 1

Lecture 4: NGS Topics – Metagenomics Part 2

Lecture 5: NGS Topics – Metagenomics Part 3

Lecture 6: NGS Topics – Transcriptomics Part 1

Lecture 7: NGS Topics – Transcriptomics Part 2

Lecture 8: NGS Topics – Transcriptomics Part 3

Lecture 9: NGS Topics – Variant Analysis Part 1

Lecture 10: NGS Topics – Variant Analysis Part 2

Lecture 11: Single-cell Data Processing Pipeline

Lecture 12: Projects Discussion and Closure

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