Long reads, real-time analysis, and native modification detection. CD Genomics' Oxford Nanopore sequencing platform delivers flexible, rapid, and comprehensive solutions for genome, transcriptome, and epigenome studies.
What we provide:
Whole-genome sequencing (standard & ultra-long), Direct RNA, full-length transcript/lncRNA profiling
Targeted sequencing (Cas9 capture or adaptive sampling) and amplicon panels
Oxford Nanopore sequencing senses changes in ionic current as single DNA or RNA molecules pass through engineered nanopores embedded in a membrane. Each short sequence context (k-mer) produces a characteristic signal ("squiggle"). These signals stream to MinKNOW, where the Dorado neural-network basecaller converts them to bases in real time. Because the molecule is read directly, native features—such as 5mC/6mA DNA methylation or RNA modifications—can be inferred from the signal without bisulfite treatment or reverse transcription.
How does nanopore sequencing work (principle):
1. A motor protein guides single-stranded DNA/RNA through a pore at a controlled rate.
2. As each k-mer resides in the pore's constriction, it modulates the current; thousands of events are recorded per second.
3. Dorado decodes the squiggle into FASTQ reads; optional raw signal files (FAST5/POD5) preserve modification information for downstream analysis.
4. Because data arrive continuously, runs can be stopped or extended on demand to meet target yield/quality.
Why it matters for research:
Ultra-long reads (hundreds of kb to Mb-class) span repeats, structural variants, telomeres/centromeres.
Real-time decision-making accelerates time-sensitive projects and optimizes flow-cell usage.
Direct RNA and native modification detection open epigenetic and transcriptomic studies with minimal bias.
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 Sequencing vs Illumina vs PacBio (HiFi)
Choosing the right platform? Here's a concise, decision-ready view of nanopore sequencing vs Illumina vs PacBio (HiFi) for research use. The comparison below helps you select the right platform for your study design.
Dimension
Oxford Nanopore (ONT)
PacBio (HiFi/SMRT)
Illumina (SBS)
Principle
Ionic-current signal through nanopores; NN basecalling (Dorado)
Optical detection in ZMWs; circular consensus (HiFi)
Sequencing-by-synthesis; optical imaging
Read length (typical)
Long; ultra-long to Mb-class possible (UL workflows)
Long; HiFi reads commonly ~15–20 kb
Short reads, typically up to 2×300 bp
Data timing
Real-time streaming; stop/extend runs on demand
Batch (consensus after run)
Batch
Native biology
Direct RNA; native DNA mods (5mC/6mA) from signal
DNA mods via kinetic signatures; RNA via cDNA
No native mod detection (standard workflows)
Accuracy paradigm
Improving raw; high consensus with depth/polishing
High per-read consensus accuracy (HiFi)
High per-base accuracy at scale
Where it shines
Ultra-long span of repeats/SVs; rapid/field work; methylation; Direct RNA
Long-read accuracy for variants and difficult regions
Large cohorts; cost-efficient small-variant depth
Trade-offs
Signal-aware informatics; per-Gb cost vs short-read
Optical platform; instrument/chemistry cost
Limited long-range context; no native mods
Quick chooser (practical rules):
Need the longest molecules (assemblies, telomeres/repeats): choose Nanopore Ultra-Long.
Need highest per-read accuracy in long reads out of the box: PacBio HiFi; or ONT with consensus/polishing per goal.
Need native modification calls or Direct RNA: Oxford Nanopore sequencing.
Large cohorts with deep SNV/indel calling: Illumina; add long reads to resolve complex loci.
Time-critical or in-field projects: Nanopore (real-time control).
Hybrid designs: combine short-read + long-read (or HiFi + ONT) to balance accuracy, cost, and long-range context.
Actual performance depends on sample integrity, library type, chemistry, 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
Input amount & integrity
Purity (guidelines)
Storage / Shipping
Key notes
Nanopore Full-Length Transcript Sequencing (cDNA)
≥500 ng–1 µg total RNA; RIN ≥8
RNA A260/280 ~2.0; A260/230 ≥2.0
Dry ice (−80 °C)
Strand-aware cDNA; Poly(A)+ or rRNA-depletion per design
Nanopore Direct RNA Sequencing
≥500 ng poly(A)+ RNA (or 1–5 µg total RNA for enrichment)*; high integrity
RNA A260/280 ~2.0; A260/230 ≥2.0
Dry ice
Preserve native mods; gentle handling; avoid RNase; no RT
Nanopore Amplicon Sequencing
≥50–200 ng pooled amplicons (≈300 bp–10 kb)
Clean PCR; no primer dimers
4 °C; cold pack
Provide primer table & target list; we can design if needed
Nanopore Full-Length lncRNA Sequencing
≥1 µg total RNA; RIN ≥8
RNA A260/280 ~2.0; A260/230 ≥2.0
Dry ice
Enrich long transcript where applicable; DNase if needed
Nanopore Targeted Sequencing — Cas9
≥1–2 µg high-quality gDNA (uncrosslinked; long fragments preferred)
DNA A260/280 1.8–2.0; A260/230 ≥2.0 (Qubit-quantified)
4 °C short; ship −20 °C on ice packs
Provide targets/gRNAs; we run in-silico specificity & on-target modeling
Nanopore Targeted Sequencing — Adaptive Sampling
≥1–2 µg gDNA; long-fragment enriched helpful
Same as above
Same as above
Provide BED/FASTA of enrich/deplete regions; no extra wet-lab capture
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.
