Oxford Nanopore sequencing uses protein nanopores embedded in a membrane to detect individual nucleotides as DNA/RNA strands pass through – measuring electrical current changes in real time. This enables:

• Ultra-long reads (10 kb to >2 Mb) for superior de novo assembly & phasing
• Real-time analysis – monitor runs live, stop/adapt as needed
• Direct sequencing of native DNA/RNA – no amplification bias, detects base modifications (e.g., methylation) natively
• Portable devices (MinION, GridION, PromethION) for field/lab flexibility

At Yaazh Xenomics, we combine Nanopore with our Illumina/MGI expertise for hybrid short + long-read projects, delivering the best of both worlds.

Our Nanopore Sequencing Platforms & Flow Cells

• MinION – Portable, flexible for small/medium projects, field sequencing
• GridION – Benchtop, up to 5 flow cells for higher throughput
• PromethION – High-throughput (up to 48 flow cells) for large genomes/cohorts
• Latest flow cells (R10.4.1 chemistry) – Up to Q30+ accuracy with improved homopolymer resolution

End-to-End Nanopore Sequencing Workflow at Yaazh Xenomics

1. Consultation & Design – Free expert guidance on project strategy, read depth, hybrid approaches
2. Sample Preparation & QC – High-molecular-weight DNA/RNA extraction (optimized for long fragments), size selection, rigorous QC
3. Library Preparation – Ligation-based (native), rapid, PCR-free options to preserve modifications
4. Real-Time Sequencing – Run on MinION/GridION/PromethION with live basecalling (Guppy/Dorado)
5. Advanced Bioinformatics Analysis (Free basic + custom):
   • Basecalling & quality filtering
   • Alignment (minimap2), variant calling (Clair3, PEPPER), structural variant detection
   • De novo assembly (Flye, Shasta), polishing (Medaka, Racon)
   • Epigenetic modification calling, full-length transcript analysis (Iso-Seq-like), metagenome binning
   • Hybrid assembly with Illumina short reads for maximum accuracy
6. Deliverables: FASTQ/POD5, BAM, assemblies, variant reports, visualizations, publication support

Key Benefits of Nanopore Sequencing with Yaazh Xenomics

• Real-time results – Monitor and adapt experiments instantly
• Ultra-long reads – Resolve complex repeats, structural variants, haplotypes
• Native modification detection – Direct methylation/epigenetic insights
• Affordable long-read access in India – Competitive pricing, no hidden costs
• Fast TAT – Efficient workflows for quicker insights
• Expert support – From sample to publication, including hybrid strategies
• ISO-certified lab – Strict QC, contamination controls, nationwide shipping

Applications of Oxford Nanopore Sequencing

• De novo genome assembly – Plants, animals, microbes, corals
• Metagenomics & microbiome – Shotgun long-read for better MAGs & functional profiling
• Human & clinical genomics – Phasing, SV detection in rare diseases/cancer
• Epigenetics – Native 5mC/6mA detection
• Transcriptomics – Full-length isoform sequencing, direct RNA
• Environmental & agricultural research – Complex community analysis
• Real-time field sequencing – Outbreak surveillance, biodiversity

Nanopore vs. Short-Read Sequencing: When to Choose Nanopore

Advantages

• Long reads resolve structural complexity short reads miss
• Real-time & portable – Ideal for rapid/on-site needs
• Detects base mods without extra steps

Limitations

• Per-base accuracy lower than Illumina (mitigated with high coverage/hybrid)
• Higher cost per base for very deep coverage

For maximum accuracy, combine with our Illumina short-read NGS.