📅 Day 1: Nanopore Sequencing Fundamentals, Basecalling & Genome Assembly
- Introduction to Long-Read Sequencing Technologies and Nanopore DNA Sequencing
- Principles of Nanopore Sequencing and Real-Time Portable Genomics
- Comparison of Nanopore Sequencing with Short-Read Sequencing Platforms
- Raw Signal Generation and FAST5/POD5 Data Formats
- AI-Based Basecalling and Signal Interpretation Using Dorado
- FASTQ Files, Read Quality Assessment, and Read Filtering
- Read Alignment Using Reference Genomes with Minimap2
- Genome Assembly from Long-Read Nanopore Sequencing Data Using Flye
- Applications in Microbial Genomics, Clinical Genomics, Agriculture, and Environmental Monitoring
🛠️ Hands-on:
- Hands-on 1: Participants will assess Nanopore sequencing read quality, read length distribution, and sequencing output using quality control tools.
- Hands-on 2: Participants will understand how long reads are assembled into draft genomes using Nanopore sequencing datasets.
📅 Day 2: AI-Assisted Genome Polishing & Metagenomic Classification
- Introduction to Genome Polishing in Long-Read Sequencing
- Sources of Errors in Nanopore Sequencing Reads
- Role of Neural Networks in Consensus Correction
- AI-Assisted Genome Polishing Using Medaka
- Importance of Polished Assemblies in Microbial Genomics
- Introduction to Metagenomics Using Nanopore Sequencing
- Real-Time Pathogen Detection and Environmental Surveillance
- AI-Supported Adaptive Sampling and Read Classification Concepts
- Taxonomic Classification of Microbial Reads
- Abundance Estimation and Microbial Community Interpretation
- Visualization of Taxonomic Classification Results
🛠️ Hands-on:
- Hands-on 3: Participants will learn how AI-assisted polishing improves genome assembly accuracy from Nanopore reads using Medaka.
- Hands-on 4: Participants will classify microbial sequencing data and visualize microbial composition using taxonomic charts.
📅 Day 3: AI-Based Variant Calling and Epigenetic Analysis
- Introduction to Genomic Variants: SNVs, Insertions, and Deletions
- Challenges of Variant Calling in Long-Read Sequencing
- Role of Deep Learning in Variant Detection
- Clair3 Architecture: Pileup and Full-Alignment Models
- Applications in Rare Disease Research, Microbial Genomics, and Clinical Genomics
- Introduction to Epigenetics and DNA Methylation
- Direct Detection of Methylation Using Nanopore Signal Data
- AI-Based Identification of 5mC, 5hmC, and 6mA Modifications
- Applications in Diagnostics, Cancer Biology, and Biopharma Research
- Visualization and Interpretation of Variant and Methylation Results
🛠️ Hands-on:
- Hands-on 5: Participants will learn how AI-based variant calling generates VCF files from Nanopore sequencing data using Clair3.
- Hands-on 6: Participants will understand how methylation signals can be detected directly from Nanopore data using Dorado/Modkit and interpreted for biological insights.
🧰 AI & Bioinformatics Tools Covered:
Participants will use selected open-source tools for Nanopore sequencing analysis, including
Dorado for AI-based basecalling and methylation detection,
NanoPlot/NanoFilt for read quality control,
Flye/Medaka for genome assembly and polishing, and
Kraken2/Bracken, Clair3, Modkit, and IGV for metagenomics, variant calling, epigenetic analysis, and genome visualization.
