The only sequencing technology that delivers Mb-class ultra-long reads, streams data in real time, and sequences native RNA directly — without reverse transcription or amplification. CD Genomics' Oxford Nanopore platform gives you the longest reads in genomics, the ability to stop a run when you have enough data, and direct access to RNA modifications that other platforms miss.
What we provide:
Ultra-long reads (Mb-class) for gap-free genome assembly and complex repeat resolution
Direct RNA sequencing — native RNA, no reverse transcription, no amplification bias
Real-time sequencing control — monitor yield live, stop when targets are met
If your project requires reads longer than 20 kb — to span large structural variants, close genome gaps, or resolve full-length transcript isoforms — Oxford Nanopore is your best option. Nanopore holds the record for the longest sequencing reads ever produced (exceeding 2 Mb). It is also the only platform that streams data in real time — allowing you to stop a run as soon as you have enough coverage — and the only platform that sequences native RNA molecules directly, preserving modification information that cDNA-based methods lose.
Of course, raw nanopore reads trade some per-read accuracy for these capabilities (typically Q10–20 raw, improving with latest chemistry and Dorado basecallers). For projects requiring the highest per-read accuracy, consider PacBio HiFi; for the longest read spans, real-time monitoring, and direct RNA analysis, Nanopore has no equal.
How Nanopore Sequencing Works
Nanopore sequencing passes a single DNA or RNA molecule through a protein nanopore embedded in an electrically resistant membrane. As each nucleotide transits the pore, it disrupts the ionic current in a sequence-specific manner. These current changes are recorded in real time and decoded into nucleotide sequences (A, T, C, G — or RNA bases) by a neural-network basecaller such as Dorado.
Unlike Illumina (sequencing-by-synthesis with cluster amplification) or PacBio (optical detection of fluorescently labeled nucleotides in zero-mode waveguides with circular consensus), Nanopore reads the native molecule directly. No amplification, no synthesis, and no optical measurement are involved. The raw signal carries not only base identity but also modification information (5mC, 6mA, and RNA modifications), which can be extracted bioinformatically without additional sample preparation.
Why it matters for your research:
Ultra-long reads (exceeding 1 Mb routinely, with record reads surpassing 2 Mb). Span telomeres, centromeres, segmental duplications, and large structural variants that cannot be resolved with short or mid-length read platforms.
Real-time data streaming. Sequencing results are generated as the molecule passes through the pore, enabling live yield monitoring, adaptive sampling (enrich or deplete target regions on-the-fly), and immediate run termination when sufficient data is collected.
Direct RNA and native modification detection. Sequence RNA molecules without reverse transcription or amplification bias. Detect DNA methylation (5mC, 6mA) from genomic reads and RNA modifications (m6A, pseudouridine, inosine) from direct RNA reads — all from the raw signal, with no bisulfite conversion or enrichment steps required.
One-line: Full-length tRNA sequencing with direct RNA modification detection on the Nanopore platform. Complete tRNA isoacceptor and isoform profiling with capture of native modifications including m1A, m3C, m7G, pseudouridine, and other epitranscriptomic marks.
One-line: Resolve complex microbial communities with long nanopore reads for species-level classification, metagenome-assembled genomes (MAGs), and resistance gene profiling. Available on both PacBio HiFi and Oxford Nanopore platforms.
Best for: Complex metagenomic communities, field-deployable metagenomics, real-time pathogen surveillance.
One-line: Sequence full-length cDNA molecules for isoform-level transcript discovery. Reverse-transcribe RNA into cDNA, then sequence directly — capturing complete transcript structures from 5' end to 3' end without assembly.
Best for: Full-length transcript isoform discovery, novel transcript identification, quantification of isoform expression.
One-line: Amplify and sequence full-length rRNA gene regions (16S, 18S, ITS) with Nanopore long reads for species-level and strain-level taxonomic resolution that short-read amplicons cannot achieve.
Best for: Microbial community profiling, environmental microbiome analysis, strain-level taxonomic classification.
What You'll Receive
Each Oxford Nanopore project is delivered with transparent data, detailed documentation, and reproducible QC metrics—ensuring publication-ready confidence.
Core data files (for every project)
FASTQ (.fastq.gz) — basecalled reads (Dorado).
Optional raw signal — FAST5/POD5 per request for modification-aware reanalysis.
Project memo — the nanopore sequencing protocol used (library kit, flow cell/chemistry, run settings), plus software versions and parameters.
Run & QC report (per sample and per barcode)
Yield & throughput: total reads/bases; pass/fail counts.
Generate long-range contact maps for scaffolding and chromatin studies.
Recommended service: Pore-C.
Metagenomics & pathogen surveillance
Improve assembly/strain resolution; benefit from real-time decisions.
Recommended services: Standard WGS, Targeted, Amplicon (per design).
For high-depth small-variant cohorts, short-read can be cost-efficient; hybrid designs (short-read + Nanopore) capture both depth and long-range context.
Nanopore vs PacBio HiFi vs Illumina — Platform Comparison
Choosing the right platform for your project? Here is how Nanopore compares to PacBio HiFi and Illumina on the dimensions that matter for research outcomes.
Dimension
Nanopore (ONT)
PacBio HiFi
Illumina
Principle
Ionic current through a protein nanopore; neural-network basecalling
Optical detection in ZMWs; circular consensus (CCS)
Sequencing-by-synthesis; cluster imaging
Read length (typical)
10–100 kb routine; ultra-long to 2 Mb+
~15–20 kb HiFi reads; subreads up to ~100 kb
Up to 2×300 bp
Per-read accuracy (raw)
Q10–Q20 raw; improving with R10.4.1 + Dorado; high accuracy with consensus depth
QV ≥30 (≥99.9%) via CCS consensus
≥99.9% raw
Data timing
Real-time streaming; stop or extend a run live
Batch (analysis after run completes)
Batch
Native biology
Direct RNA sequencing; 5mC/6mA from raw signal; RNA modifications without RT or amplification
5mC from polymerase kinetics; no bisulfite needed
No native modification detection (standard workflows)
Where it shines
Ultra-long span (telomeres, massive SVs, gap closure); real-time/field work; Direct RNA
Highest long-read accuracy; assemblies and methylation from one dataset
Deep SNV/indel cohorts; cost-efficient large studies
Trade-offs
Raw accuracy lower than HiFi or Illumina; signal-aware bioinformatics required
Longer run times; no real-time control or streaming
No long-range context; cannot detect native modifications
Quick decision guide:
Need reads longer than 100 kb or field-deployable sequencing → Nanopore.
Need the highest accuracy in long reads for assemblies and variant calling → PacBio HiFi.
Need direct RNA sequencing or real-time data → Nanopore is the only option.
Large SNV/indel cohorts on a budget → Illumina for depth; add Nanopore long reads for SVs and phasing.
Hybrid designs: Nanopore ultra-long + PacBio HiFi for complete T2T assemblies; Nanopore long reads + Illumina short reads for SV detection with deep SNV validation.
Actual performance varies with sample quality, library preparation, sequencing depth, and analysis pipeline.
Quality & Study Design
Replicates & Controls: Recommend ≥2 biological replicates per condition; include negatives for amplicon/targeted; optional spike-ins for methylation.
Coverage Planning: Size long-read depth to genome complexity/SV goals; plan on-target depth for targeted/amplicon; size reads/sample for isoforms or Direct RNA.
Acceptance Criteria: Pre-agreed targets for yield per barcode, on-target fraction, mapping rate, and read-length profile (e.g., N50 goals for Ultra-Long).
Run-Time Decisions: Use real-time dashboards to stop/extend/reload efficiently; document any variances in the project memo.
The CD Genomics Advantage
1
Applications-first scoping
Map your biological question to the right Oxford Nanopore service (Ultra-Long, Direct RNA, Full-Length Transcript/lncRNA, Targeted/Cas9 or adaptive, Amplicon, Pore-C, TAIL Iso-Seq).
2
Design modeling & feasibility
Coverage modeling, barcode balance, and target/primer feasibility checks before you commit.
3
Reproducible analytics
Containerized/ version-locked pipelines; clean result packaging with analysis report and data dictionary.
4
Real-time run efficiency
Live dashboards to stop/extend/reload when goals are met; adaptive sampling when suitable.
5
Data integrity & security
Structured folders, checksum verification, and secured transfer with a stated retention policy.
6
Publication-grade support
Optional results walkthrough, figure/table preparation, and manuscript/review assistance.
7
Cross-platform neutrality
Objective guidance when hybrid strategies (short-read + ONT, or HiFi + ONT) add value.
Sample Requirements
Service
Amount & Integrity
Purity
Storage / Shipping
Key Notes
WGS (Standard)
≥1–3 μg gDNA, ≥30 kb
A260/280 1.8–2.0; A260/230 ≥2.0
−20°C on ice
Provide extraction method; no vortexing
Ultra-Long WGS
≥3–5 μg HMW gDNA, ≥50 kb preferred
A260/280 1.8–2.0; A260/230 ≥2.0
−20°C
Gentle handling critical; wide-bore tips only
Direct RNA Sequencing
≥500 ng–1 μg poly(A)+ RNA; RIN ≥7
A260/280 ~2.0; A260/230 ≥2.0
−80°C dry ice
Do not heat or denature before shipping
Full-Length Transcript
≥500 ng–1 μg total RNA; RIN ≥8
A260/280 ~2.0; A260/230 ≥2.0
−80°C dry ice
Poly(A)+ or rRNA-depleted per design
Full Length LncRNA
≥500 ng–1 μg total RNA; RIN ≥7
Same as above
−80°C dry ice
rRNA depletion or poly(A)– selection
Amplicon Sequencing
≥50–200 ng pooled amplicons
Clean PCR; no primer dimers
4°C cold pack
Provide primer table and target gene
Targeted (Cas9/Adaptive)
≥1–3 μg gDNA
A260/280 1.8–2.0
−20°C
Provide target region BED file or gene list
Pore-C
≥1–2 μg HMW gDNA, ≥50 kb
A260/280 1.8–2.0
−20°C
Gentle handling; no vortexing
TAIL Iso-Seq
≥500 ng–1 μg total RNA; RIN ≥7
A260/280 ~2.0
−80°C dry ice
Poly(A)+ selection required
Nano tRNA Sequencing
≥500 ng total RNA; RIN ≥7
A260/280 ~2.0; A260/230 ≥2.0
−80°C dry ice
Provide tRNA enrichment method if self-enriched
Long Reads Amplicon
≥100 ng pooled amplicons; ≥500 bp target
Clean PCR; no primer dimers
4°C cold pack
Provide primer table + target coordinates
General notes
Avoid inhibitors (phenol, heparin, EDTA, polysaccharides) and repeated freeze–thaw; do not over-dry beads.
Use wide-bore tips and no vortexing for HMW DNA.
Include a brief extraction method and any known contaminants.
Low-input/FFPE or unusual matrices may be feasible—contact us for a customized protocol.
Authors: Bin Sun, Kaushal Kumar Bhati, Peizhe Song, et al.
Publication date: September 27, 2022
Journal: PLOS Genetics
Research question (Attention):
Which enzyme installs m^6A at the 3′UTR of the FLOWERING LOCUS C (FLC) mRNA, and how does that modification affect FLC transcript stability and flowering?
Approach:
A multi-omics design integrated Oxford Nanopore Direct RNA sequencing, mRNA-seq, and meRIP-seq to profile differential expression and differential RNA methylation in wild type vs FIONA1 (FIO1) mutant plants. Direct RNA captured native signal features while meRIP-seq mapped m^6A-enriched regions; combined evidence pinpointed the modification site at the FLC 3′UTR.
Key findings:
FIO1 is the methyltransferase responsible for 3′UTR m^6A on FLC mRNA.
Loss of this 3′-end methylation in fio1 mutants destabilizes FLC mRNA (reduced FLC levels) and contributes to an early-flowering phenotype.
The authors released Nanopore Direct RNA data (GEO: GSE212766) and matched mRNA/meRIP datasets, supporting reproducibility.
Direct RNA-sequencing analysis.
What this demonstrates:
This peer-reviewed study shows how Nanopore Direct RNA sequencing—paired with analysis of RNA modifications (m^6A)—answers biological questions that depend on native RNA and post-transcriptional regulation. It's a strong exemplar of "nanopore sequencing technology, bioinformatics, and applications" for epitranscriptomics and gene-regulatory mechanisms.
How CD Genomics would scope a similar project:
Service: Nanopore Direct RNA Sequencing (+ optional meRIP-seq via partner workflow)
Analysis: isoform profiling, modification-associated signal summaries, differential expression, integration with immunoprecipitation-based m^6A peaks
Sample Submission Guidelines
Direct RNA-sequencing analysis.
