Nanopore Genomics 2.0: Structural Variants, Native Epigenomics & Clinical Metagenomics

To provide participants with practical, research-oriented training in Oxford Nanopore long-read data analysis, with a focus on structural variants, native epigenomics, transcriptomics, clinical metagenomics and AMR-related genomic interpretation.

• Understand modern Oxford Nanopore sequencing data workflows
• Evaluate long-read sequencing quality, mapping and coverage
• Detect and interpret structural variants from nanopore datasets
• Understand complex genomic regions, repeat expansions and haplotype-aware analysis
• Explore adaptive sampling and targeted sequencing concepts
• Analyse native DNA methylation from nanopore reads
• Understand long-read transcript and isoform profiling
• Perform nanopore-based microbial and metagenomic classification
• Identify pathogens and antimicrobial-resistance determinants
• Visualize genomic and epigenomic results using IGV
• Build reproducible nanopore bioinformatics workflows for research applications

📅 Day 1: Long-Read Human Genomics & Structural Variant Discovery

• Focus: Understanding how nanopore long reads enable detection and interpretation of genomic variation that may be difficult to resolve using short-read sequencing.
• Understanding the nanopore analysis workflow: POD5 → Basecalling → FASTQ/BAM → Alignment → Variant Analysis.
• Evaluating read quality using Q-score, N50, sequencing coverage, read length, and mapping statistics.
• Performing long-read genome alignment and exploring reference-based genomic analysis.
• Detecting structural variants including deletions, insertions, duplications, inversions, and translocations.
• Understanding copy-number variation, repeat expansions, and difficult-to-map genomic regions.
• Introduction to haplotype phasing, allele-specific variation, and complex genomic interpretation.
• Applications of long-read structural-variant analysis in rare disease, cancer, and clinical genomics.

🛠️ Hands-on:

• Structural variant discovery from a public nanopore human genome dataset, including read QC, alignment, variant calling, and genome visualization.

🧰 Tools Covered: NanoPlot, Minimap2, SAMtools, Sniffles2, IGV, Python, Google Colab

🎯 Deliverable: Long-read QC report, structural-variant table, and genomic visualization of selected variants.

📅 Day 2: Native DNA Methylation, Adaptive Sampling & Long-Read Transcriptomics

• Focus: Exploring how nanopore sequencing enables real-time targeted sequencing, direct DNA methylation detection, and full-length transcript analysis.
• Introduction to adaptive sampling and real-time selective nanopore sequencing.
• Understanding target enrichment, host-DNA depletion, and targeted sequencing strategies.
• Native DNA methylation analysis and direct detection of 5mC using nanopore sequencing.
• Working with modified-base BAM files and analysing CpG-level methylation patterns.
• Understanding haplotype-resolved methylation and integration of genetic and epigenetic information.
• Comparing cDNA and direct RNA nanopore sequencing approaches.
• Exploring full-length transcripts, transcript isoforms, and alternative splicing.
• Applications in cancer genomics, rare disease, functional genomics, and epigenomics research.

🛠️ Hands-on:

• Nanopore native DNA methylation analysis with haplotype-aware genomic interpretation and visualization.

💡 Mini-Demo:

• Long-read transcript and isoform profiling using nanopore RNA sequencing concepts.

🧰 Tools Covered: Dorado Concepts, Modkit, Minimap2, SAMtools, IGV, BEDTools Concepts, Python, Google Colab

🎯 Deliverable: Regional methylation profile with genomic and epigenomic visualization and interpretation.

📅 Day 3: Clinical Metagenomics, Pathogen Genomics & AMR Profiling

• Focus: Using nanopore sequencing for microbial identification, pathogen genomics, antimicrobial-resistance profiling, and clinical metagenomic interpretation.
• Introduction to nanopore sequencing applications in microbial genomics and infectious-disease research.
• Understanding shotgun metagenomics versus targeted sequencing approaches.
• Real-time pathogen identification from nanopore sequencing data.
• Detection and interpretation of bacterial, viral, and fungal sequences.
• Taxonomic classification and species-level microbial interpretation.
• Long-read microbial genome assembly and reconstruction.
• Analysis of plasmids, mobile genetic elements, and genome-associated resistance determinants.
• Identification of antimicrobial-resistance genes and resistance-associated mutations.
• Understanding pathogen–AMR associations for genomic surveillance and clinical research.
• Clinical metagenomics quality control, contamination, false-positive interpretation, and reporting considerations.
• Introduction to reproducible nanopore bioinformatics pipelines and Nextflow workflow concepts.

🛠️ Hands-on:

• Pathogen identification and antimicrobial-resistance profiling using a public nanopore metagenomic dataset.

🧰 Tools Covered: Kraken2, Minimap2, Flye, AMRFinderPlus / ResFinder Concepts, IGV, Nextflow Concepts, Python, Google Colab

🎯 Deliverable: Microbial taxonomic profile, pathogen summary, AMR profile, and research-ready genomic analysis report.

• Students from biotechnology, bioinformatics, genetics, microbiology, molecular biology and life sciences
• Ph.D. scholars and researchers working in genomics, epigenomics, transcriptomics, metagenomics or AMR research
• Faculty members and academicians interested in advanced sequencing and bioinformatics workflows
• Professionals from biotechnology, diagnostics, clinical research, genomic surveillance and sequencing-based R&D
• Learners who want to move beyond basic sequencing and explore modern long-read genomic analysis

• Process and analyse nanopore long-read sequencing data
• Generate long-read QC reports and mapping summaries
• Identify candidate structural variants using nanopore bioinformatics tools
• Interpret methylation profiles and epigenomic patterns
• Understand targeted sequencing and adaptive sampling workflows
• Explore long-read transcriptomics and isoform-level analysis
• Perform microbial taxonomic profiling from nanopore metagenomic data
• Screen pathogen data for AMR-associated determinants
• Prepare research-ready genomic, epigenomic and metagenomic analysis summaries