Ready to decode complex genomes? This mentor-led virtual workshop provides advanced, research-oriented training in Oxford Nanopore bioinformatics workflows. Move beyond basic sequencing and learn to convert long-read data into meaningful genomic, epigenomic, and microbiological insights.
📚 Workshop Structure & Topics:
Day 1: Long-Read Human Genomics & Structural Variant Discovery • Focus: Detecting genomic variation difficult to resolve with short-read sequencing. • Workflow: POD5 → Basecalling → FASTQ/BAM → Alignment → Variant Analysis. • Key Skills: Read QC (Q-score, N50, coverage), genome alignment, and detecting structural variants (deletions, insertions, duplications, inversions, translocations), CNVs, and repeat expansions. • Hands-on Tools: NanoPlot, Minimap2, SAMtools, Sniffles2, IGV, Python, Google Colab. • Deliverable: Long-read QC report, structural-variant table, and genomic visualization.
Day 2: Native DNA Methylation, Adaptive Sampling & Long-Read Transcriptomics • Focus: Real-time targeted sequencing, direct DNA methylation detection, and full-length transcript analysis. • Key Skills: Adaptive sampling, host-DNA depletion, analyzing modified-base BAM files for 5mC/CpG-level methylation, haplotype-resolved methylation, and comparing cDNA vs. direct RNA sequencing for isoform profiling. • Hands-on Tools: Dorado Concepts, Modkit, Minimap2, SAMtools, IGV, BEDTools Concepts, Python, Google Colab. • Deliverable: Regional methylation profile with genomic/epigenomic visualization.
Day 3: Clinical Metagenomics, Pathogen Genomics & AMR Profiling • Focus: Microbial identification, pathogen genomics, and antimicrobial-resistance (AMR) profiling. • Key Skills: Shotgun vs. targeted metagenomics, taxonomic classification, long-read microbial genome assembly, plasmid/mobile genetic element analysis, and identifying AMR genes/mutations. • Hands-on Tools: Kraken2, Minimap2, Flye, AMRFinderPlus / ResFinder Concepts, IGV, Nextflow Concepts, Python, Google Colab. • Deliverable: Microbial taxonomic profile, pathogen summary, AMR profile, and research-ready analysis report.
🎯 Who Should Attend? Students, Ph.D. scholars, researchers, faculty, and industry professionals in bioinformatics, genomics, epigenomics, transcriptomics, metagenomics, microbiology, and clinical research.
🏆 Learning Outcomes: Participants will walk away with the ability to process nanopore data, generate QC reports, identify structural variants, interpret methylation profiles, perform microbial taxonomic profiling, screen for AMR determinants, and build reproducible bioinformatics pipelines.
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