Oxford Nanopore Sequencing Technology — Comprehensive Long-Read Genomics Services

At a glance:

• The Long-Read Genomics Imperative
• How Nanopore Sequencing Works
• ONT Platforms at CD Genomics
• ONT Services by Research Application
• ONT vs Other Sequencing Technologies
• Sample Requirements for ONT Sequencing
• Bioinformatics and Data Delivery
• Frequently Asked Questions

How Nanopore Sequencing Works — Direct, Real-Time Molecular Detection

ONT sequencing is fundamentally different from sequencing-by-synthesis. There are no polymerases, no fluorescent labels, and no amplification cycles. Instead, a motor protein guides a single DNA or RNA strand through a protein nanopore embedded in an electrically resistant membrane. As each nucleotide passes through the pore's constriction point, it disrupts the ionic current in a characteristic way. An ASIC chip underneath the membrane measures these current fluctuations at high frequency, and a basecalling algorithm — typically a recurrent neural network or transformer model — converts the raw signal trace into nucleotide sequence in real time.

This direct detection architecture confers several capabilities that synthesis-based platforms cannot replicate. Because ONT reads the native molecule, it captures base modifications — 5-methylcytosine (5mC), N6-methyladenosine (m6A), pseudouridine — without bisulfite conversion or antibody enrichment. Because there is no amplification, GC bias is minimal. And because each molecule threads through independently, the platform streams data continuously, allowing researchers to stop a run as soon as sufficient coverage is reached.

The current R10.4.1 nanopore chemistry, combined with duplex basecalling, delivers consensus accuracy exceeding Q20 (99% raw read accuracy), with some applications achieving Q30+ through computational polishing. Read lengths routinely reach 50-100 kb for standard genomic DNA preparations, and ultra-long protocols can yield individual reads exceeding 1 Mb. At CD Genomics, we have validated these performance characteristics across all three ONT platforms, ensuring that every project — from a single MinION flow cell to a full PromethION 48 — benefits from consistent, production-grade data quality.

ONT Services by Research Application

This is where you find the exact ONT service for your project. CD Genomics delivers 45+ application-specific ONT sequencing services organized by research area. Each linked service page includes detailed workflows, sample requirements, bioinformatics deliverables, and case studies where applicable.

Human Genomics with Long-Read Sequencing

ONT's long reads resolve medically relevant genomic regions — HLA loci, segmental duplications, repeat expansions — that short reads routinely miss. Our human genomics services include:

• Human Leukocyte Antigen (HLA) Typing — Full-length, phased HLA genotyping across all class I and II genes, eliminating ambiguity from short-read imputation.
• Human Whole Genome Sequencing — 30× ONT long-read WGS with structural variant calling and haplotype phasing for rare disease and cancer research.
• Human Long-Amplicon Sequencing — Targeted amplicons up to 20 kb for repeat expansion disorders, pharmacogene panels, and complex locus characterization.
• Human Mitochondrial DNA Sequencing — Full-length mtDNA sequencing with heteroplasmy detection down to 1% minor allele frequency.
• Human Genome Structural Variation Detection — Comprehensive SV calling (>50 bp insertions, deletions, inversions, duplications, translocations) from ONT long reads.
• Full-Length TCR/BCR Repertoire Profiling — Complete V(D)J region sequencing for immune repertoire diversity analysis without assembly.

For an overview of all human long-read sequencing services, visit our Human Genomics with Long-Read Sequencing hub.

Animal and Plant Genomics with Long-Read Sequencing

Large, repetitive, and polyploid genomes — common in plants and many animals — are where ONT truly excels. Ultra-long reads span centromeres, telomeres, and ribosomal DNA arrays that fragment in short-read assemblies.

• Animal/Plant Whole Genome Sequencing — Resequencing with ONT long reads for SV detection, allele phasing, and population genomics.
• Animal/Plant Whole Genome De Novo Sequencing — High-contiguity genome assembly using ONT ultra-long reads, routinely achieving chromosome-scale scaffolds.
• Animal/Plant Long Amplicon Sequencing — Targeted long-range PCR products for resistance gene clusters, biosynthetic gene clusters, and QTL fine-mapping.
• Animal/Plant RNA Sequencing — Full-length transcript isoform identification and quantification in non-model species.
• Pan-Genome Analysis — Multi-sample ONT assemblies to capture presence/absence variation and structural diversity across populations.
• Mitochondrial/Chloroplast Genome Sequencing — Complete organellar genome assembly without the need for organelle enrichment.
• SSRs/STRs Analysis — Accurate microsatellite genotyping from long reads, avoiding PCR stutter artifacts.
• Haplotype-resolved T2T Genome Assembly — Phased, telomere-to-telomere assemblies that resolve both parental haplotypes independently.
• T2T Genome Assembly — Complete genome assembly including centromeres, telomeres, and rDNA arrays — no gaps.

Browse all services in our Animal and Plant Genomics with Long-Read Sequencing hub.

Microbial Genomics with Long-Read Sequencing

ONT enables complete, closed microbial genomes — including plasmids — in a single sequencing run. Real-time data streaming also supports rapid pathogen identification and antimicrobial resistance profiling.

• Bacterial Whole-Genome Resequencing — Complete circular bacterial genomes with plasmid resolution and AMR gene identification.
• Fungal Whole-Genome Resequencing — Long-read WGS for fungal species with large, repeat-rich genomes.
• Viral Whole-Genome Resequencing — Full-length viral genome sequencing, including quasispecies analysis and mutation tracking.
• Bacterial Whole-Genome De Novo Sequencing — Complete, closed genome assembly for novel bacterial isolates without a reference.
• Fungal Whole-Genome De Novo Sequencing — De novo assembly of fungal genomes with chromosome-level contiguity.
• Viral Genome De Novo Sequencing — Novel virus discovery and complete genome characterization from clinical or environmental samples.
• Long-Read Metagenomics Sequencing — Species-level taxonomic resolution and functional profiling without assembly, directly from complex communities.
• Full-Length 16S/18S/ITS Amplicon Sequencing — Complete rRNA gene sequencing for strain-level microbial community profiling.
• Full-Length Plasmid Sequencing — Complete plasmid characterization including size, structure, resistance cassettes, and replication origins.
• Antibiotic Resistance Gene (ARG) Analysis — Comprehensive ARG detection and characterization with genomic context from long reads.
• Nanopore Bacterial Direct RNA Sequencing — Native bacterial transcriptome profiling with modification detection — no reverse transcription.

See the full catalog at our Microbial Genomics with Long-Read Sequencing hub.

Transcriptomics with Long-Read Sequencing

Short-read RNA-seq quantifies gene expression at the level of counts per gene. It tells you a gene is upregulated, but not which isoform. ONT reads full-length cDNA or native RNA molecules, revealing the complete isoform landscape — alternative splicing, alternative polyadenylation, fusion transcripts, and RNA modifications — in a single experiment.

• circRNA Full-Length Identification and Quantification — Complete circular RNA characterization with full-length sequence and junction validation.
• Poly(A) Tail Length Analysis — Direct measurement of poly(A) tail length distribution from native RNA or cDNA — no enzymatic tailing.
• Nanopore Direct lncRNA Sequencing — Full-length long non-coding RNA identification and quantification without assembly.
• Kinnex Full-Length RNA-seq — Concatenated cDNA sequencing with ~16x throughput boost for cost-effective isoform-level transcriptomics.
• Nanopore Direct RNA Sequencing — Native RNA molecules sequenced directly through the nanopore, preserving modification information and eliminating RT bias.
• Nanopore Full-Length cDNA Sequencing — PCR-cDNA sequencing for high-yield isoform discovery when RNA input is limited.
• Full-Length Transcriptome Profiling — Combined long-read isoform sequencing with short-read quantification for hybrid, publication-ready transcriptomics.
• Full-Length Spatial-Temporal Transcriptome Profiling — Isoform-level expression across tissues, developmental stages, or conditions.
• Single-Cell Full-Length Transcriptome Sequencing — Per-cell isoform expression, differential splicing, and fusion transcript detection using MAS-seq/Kinnex.
• Nano tRNA Sequencing Service — Native tRNAome profiling with modification detection — uniquely enabled by ONT direct RNA sequencing.
• Nanopore Ribosome tRNA Sequencing — Ribosome-associated tRNA profiling for translation dynamics research.

Explore all transcriptomics services at our Transcriptomics with Long-Read Sequencing hub.

Epigenetics and Methylation Analysis Using Long-Read Sequencing

Because ONT detects base modifications directly from the electrical signal during sequencing, it eliminates the need for bisulfite conversion, which degrades DNA and introduces bias. The same sequencing run simultaneously yields sequence, 5mC, 5hmC, and, for RNA, m6A and pseudouridine information.

• ONT-gDNA-RRMS — Reduced-representation methylation sequencing with ONT for cost-effective, genome-wide 5mC profiling.
• Long-Read Sequencing of DNA Methylation — Whole-genome 5mC and 5hmC detection at single-molecule, single-nucleotide resolution.
• Long-Read Sequencing of RNA Methylation — Direct RNA modification detection (m6A, pseudouridine, inosine) without antibody enrichment or chemical treatment.
• Fiber-seq Service — Chromatin fiber analysis via ONT for long-range nucleosome positioning, chromatin accessibility, and DNA methylation on individual molecules.

Visit our Epigenetics and Methylation Analysis hub for complete details.

Whole-Genome Resequencing with Long-Read Sequencing

When you already have a reference genome and need to characterize population-level variation or identify causal mutations, ONT resequencing delivers the complete variant spectrum — SNVs, indels, and structural variants — in one workflow.

• Variant Calling — Comprehensive SNV, indel, and SV detection from ONT data with haplotype phasing.
• Genome-Wide Association Study (GWAS) — Long-read-powered GWAS that captures structural variant associations missed by SNP arrays and short reads.
• Population Evolution — Comparative population genomics leveraging SVs and repeat expansions as evolutionary markers.
• Nanopore Targeted Sequencing — ONT-based targeted enrichment and long-read sequencing of specific genomic regions, gene panels, or custom loci with full-length resolution and modification detection.

All resequencing services are listed at Whole-Genome Resequencing with Long-Read Sequencing.

Pre-Made Library Long-Read Sequencing Services

If you have already prepared sequencing libraries and only need instrument time and data delivery, we offer library-only sequencing on both ONT and PacBio platforms.

• PacBio Pre-Made Library Sequencing — Submit your prepared SMRTbell libraries for HiFi sequencing on the Revio system.
• Oxford Nanopore Pre-Made Library Sequencing — Submit your prepared ONT libraries for sequencing on our GridION or PromethION systems.

See both options at Pre-Made Library Long-Read Sequencing Services.

Long-Read Sequencing Data Analysis Services

Sequencing is only half the story. Our bioinformatics team provides end-to-end analysis for ONT data, from basecalling through biological interpretation.

• PacBio Sequencing Data Analysis — Custom bioinformatics for HiFi data: genome assembly, variant calling, methylation analysis, isoform quantification.
• Oxford Nanopore Sequencing Data Analysis — ONT-specific bioinformatics: Dorado/Guppy basecalling, minimap2 alignment, Clair3/DeepVariant variant calling, Flye/Canu assembly, Modkit modification calling.

Visit Long-Read Sequencing Data Analysis Services for detailed analysis packages.

Sample Requirements for ONT Sequencing

ONT sequencing performance depends critically on input nucleic acid quality, particularly molecular weight for DNA applications. Below are general guidelines; specific services may have additional requirements detailed on their respective pages.

For detailed protocols, shipping instructions, and application-specific requirements, consult our Sample Submission Guideline. Our project managers review every submission and will contact you if additional material or preparation is needed.

Frequently Asked Questions

For research use only. Not for use in diagnostic procedures.