Nanopore Amplicon Sequencing

Overview

Nanopore-based Amplicon Sequencing enables targeted sequencing of specific genomic or plasmid regions with high flexibility and speed. Leveraging long-read capabilities, this service allows accurate characterization of amplicons ranging from short fragments to multi-kilobase regions, including repetitive or structurally complex targets. This service is well suited for mutation analysis, variant confirmation, microbial identification, and targeted validation studies.

Monday Promotion

Offer:

Amplicon Standard: $9.99/sample

Amplicon Pro: $19.99/sample

Terms and Conditions:

• The promotional pricing applies to all qualifying Nanopore Sequencing orders placed every Monday, based on ET.

• The discount will be applied automatically when you place your order through the QuinGo online portal.

• Quintara Biosciences reserves all rights to this promotion.

Easy submission with >1,000 drop boxes in the US
Free same-day sample pick-up
Flat price, cost-effective, and no hidden fees
Overnight data delivery. Processing available 7 days a week for maximum scheduling flexibility
Flexible amplicon length
Primer-Free, enabling fast and easy submission

What Is Amplicon Sequencing Used For?

Gene Editing and Validation

Targeted Sequencing

Pathogen Monitoring and Surveillance

Precision Medicine and Clinical Applications

• CRISPR/Cas9 Edit Verification

• Gene Knock-In/Knock-Out Confirmation

• Point Mutations and Small Variants Detection

• Full-length Gene Sequencing

• Structural Variant Analysis

• Targeted Pathogen Genotyping

• Microbial Strain Differentiation

• Species Detection in Environmental Samples

• Biodiversity Monitoring

• Targeted Cancer Mutation Profiling

• Mutation Detection in Hereditary Disorders

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Workflow

Quintara delivers a fully integrated, end-to-end sequencing solution. From the moment your DNA samples arrive, processing begins immediately at the closest regional site—ensuring fast, local turnaround. Every sample is prepared and sequenced by our expert scientists using optimized workflows on the latest Oxford Nanopore platforms, then analyzed through tailored bioinformatics pipelines for precise, actionable results.

Sample Submission
No primers required
Accepts purified and unpurified samples
1,000+ drop boxes
Library Preparation
ONT library prep workflows
Quintara’s proprietary workflows
Sequencing
ONT long-read technology
Ultra-high coverage depth
Real-time data acquisition
Data Analysis
Data processing and alignment
Variant analysis and quality assessment
Ready-to-use deliverables

Services

Service Name	Size	Sample Type	Price	Turnaround Time*
AmpValueComing Soon	100bp - 5kb	Unpurified PCR Product; Purified PCR Product	$3.99⁺	Overnight
AmpStandardUpgrade	500bp - 25kb		$15.00	Overnight
AmpPro	100bp - 25kb		$30.00	Overnight

*Your project clock starts once we receive your samples.

+The listing price of AmpValue service is Beta testing price.

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Choose the Services According to Your Needs

	AmpValue Overnight $3.99*	AmpStandard Overnight $15	AmpPro Overnight $30
Designed For	Budget-friendly option for sequencing short to medium-length amplicons. Ideal for high-throughput projects.	Classic long-read sequencing for clonal amplicons of any length. Ideal for routine amplicon verification	Deep sequencing with full-length reads for resolving amplicon mixtures. Ideal for amplicon library verification.
Sample Size	200bp - 5kb	500bp - 25kb	100bp - 25kb
Sample Input	Unpurified PCR product (20μL, 50-100ng/μL) Purified PCR product (10μL, 30-100ng/μL)	Unpurified PCR product (10μL, 20-100ng/μL) Purified PCR product (10μL, 20-100ng/μL)	Unpurified PCR product (20μL, 1 ng/μl per 100bp) Purified PCR product (20μL, 1 ng/μl per 100bp)
Coverage	Up to 1,000 reads	Up to 1,000 reads	Up to 4,000 reads
Variants/Sample	1 - 3	1	10 – 200+
Deliverables	• FASTA File • AB1 File (chromatogram)	• FASTA File • AB1 File (chromatogram) • Genbank File • Per-Base Data File • Raw Data FASTQ File • QC Report • Alignment File • Summary File and Report	• FASTA File • AB1 File (chromatogram) • Genbank File • Per-Base Data File • Raw Data FASTQ File • QC Report • Alignment File • Summary File • Variant Analysis Results

* Beta testing price

FAQ

What are the requirements for submitting PCR samples?: Please provide us with 10-20 µL of your undiluted sample. Before submission, please verify the quality of your PCR products by running them on a gel. Though magnetic beads or column-based purification is not a mandatory step, we strongly encourage purifying your samples before submission, as it significantly reduces the likelihood of reaction failure. High concentrations are a must when sequencing linear DNA. We don’t recommend submitting your sample if you notice a dim band or multiple bands on the gel.

What is included in the data package for Nanopore Amplicon Sequencing?

For both Amplicon-Standard and Amplicon-Pro services

The sequencing results include:

• Chromatogram (ab1) files: Sanger-like trace files derived from Nanopore data

• FASTA files: Universal format for sequence alignment

• GenBank files: Annotated using the pLannotate library, compatible with tools like SnapGene Viewer

• Per-base breakdown: CSV file with quality scores and low-confidence base calls

• QC report: PDF summarizing purity, read length distribution, multimer percentage, mapping statistics, and more

• Raw FASTQ files: Full sequencing reads •Multi-alignment FASTA files

• Virtual Gel Image: Image representing sequence quality and alignment

• Excel summary: Overview of sequencing statuses for all samples in the order

For Amplicon-Pro, there is an additional type of file: the FASTA variant files.

How do I prepair my samples for Nanopore Amplicon sequencing?

For Amplicon-Standard: (0.5kb - 25kb)

• Unpurified Amplicon Product:

Required concentration: 20–100 ng/µL, Volume: >10 µL, Container: 200μl strip tubes
(Note: High failure rates compared to submitting purified PCR products.)

• Purified Amplicon Product:

Required concentration: 20–100 ng/µL, Volume: >10 µL, Container: strip tubes

For Amplicon-Pro: (0.1kb to 25kb)

• Unpurified Amplicon Product:

Required concentration: 1 ng/μl per 100bp, Volume: >20 µL, Container: 200μl strip tubes
(Note: High failure rates compared to submitting purified PCR products.)

• Purified Amplicon Product:

Required concentration: 1 ng/μl per 100bp, Volume: >20 µL, Container: 200μl strip tubes

What is the typical turnaround time for Nanopore Amplicon sequencing?: For Amplicon-Standard and Amplicon-Pro services, the turnaround time is next morning for all types of samples upon receipt.

Do you provide raw FASTQ files for Nanopore Amplicon sequencing?

Yes, for Amplicon-Standard and Amplicon-Pro services, we provide raw FASTQ files in the data package.

These files are widely used for downstream analysis and can be processed with various bioinformatics tools.

Do you provide a QC report for Nanopore Amplicon sequencing?: Yes, we provide a QC report for all Amplicon-Standard and Amplicon-Pro orders. This includes metrics on read length distribution, purity, multimer percentage, mapping statistics, and more.

What is the typical coverage for amplicon sequencing, and how does it impact data quality?: The typical coverage for amplicon sequencing is >500x for Amplicon-Standard and can reach 4000x or higher for Amplicon-Pro, depending on the sample and sequencing conditions. Higher coverage generally improves the accuracy of the sequencing results by increasing the number of reads that cover each base in the amplicon, which reduces errors and enhances the confidence in detecting variants. Insufficient coverage may lead to lower-quality data, making it harder to detect rare variants or accurately assemble the sequence. Ensuring adequate coverage is crucial for reliable results, especially when analyzing complex or low-abundance targets.

Can I submit mixed amplicons in the same sample, and how will the data be processed?

• For Amplicon-Pro, when multiple amplicons are submitted in the same sample, we provide multiple final consensus sequences, each representing a specific amplicon in the sample. Additionally, raw FASTQ files are provided, which represent the sequencing data for the mixed samples as a whole. You can use these raw files to analyze each amplicon independently if needed.

• For Amplicon-Standard, only one final consensus sequence will be returned, even if multiple amplicons are submitted in the same sample. The raw FASTQ files provided represent the mixed sequencing data for all amplicons in the sample, allowing you to analyze the data further.

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