Why Choose Nanopore Amplicon Sequencing?

Conventional short-read sequencing targets only partial gene regions, which can make it difficult to distinguish closely related species or resolve complex genetic variations. Nanopore Amplicon Sequencing overcomes these limitations by generating full-length amplicon reads, enabling more accurate taxonomic classification, variant detection, and genomic analysis.

Long-read sequencing of complete 16S rRNA, ITS, and custom gene targets improves species- and strain-level identification while reducing ambiguity in microbial community profiling, pathogen surveillance, and clonal validation studies.

Technical Specifications

N2Jenomics Lab Pvt. Ltd. offers a complete Nanopore Amplicon Sequencing workflow optimized for both single-amplicon and complex microbial community analyses.

Quality Assurance

Every project includes rigorous quality control, including DNA quality assessment, sequencing performance evaluation, read-length distribution analysis, and data validation to ensure reliable results.

Applications

Nanopore Amplicon Sequencing supports a wide range of research and clinical applications by providing complete amplicon sequences for accurate downstream analysis.

• Microbial Community Profiling

• - Full-length 16S rRNA and ITS sequencing
• - Species- and strain-level microbial identification
• - Microbiome diversity and comparative analysis

• Pathogen Detection

• - Identification of microbial pathogens
• - Environmental and clinical surveillance
• - Food, water, and agricultural biosafety monitoring

• Food & Agricultural Research

• - Characterization of beneficial and harmful microorganisms
• - Crop microbiome studies
• - Agricultural biotechnology and breeding programs

• Clonal Verification & Variant Analysis

• - Validation of plasmids and engineered constructs
• - Mutation and variant confirmation
• - High-confidence consensus sequence generation

• Comparative Genomics

• - Strain differentiation
• - Population genetics studies
• - Evolutionary and phylogenetic analysis

Workflow

Our streamlined workflow delivers high-quality sequencing data from sample submission to final analysis.

1. Target Selection

Design primers for full-length 16S rRNA, ITS, or custom amplicon targets.

2. PCR Amplification

Generate high-quality amplicons using optimized PCR protocols with optional sample barcoding.

3. Library Preparation

Prepare sequencing libraries using Oxford Nanopore Kit 14 with minimal DNA fragmentation.

4. Nanopore Sequencing

Sequence libraries on PromethION or GridION platforms using R10.4.1 flow cells.

5. Data Processing

Perform basecalling, quality filtering, consensus generation, and chimera removal.

6. Bioinformatics Analysis

Conduct taxonomic classification, variant identification, diversity analysis, and generate comprehensive reports.

7. Data Delivery

Receive FASTQ/FASTA files, quality control reports, taxonomic summaries, variant tables, and publication-ready HTML/PDF reports.

Bioinformatics Analysis & Reporting

N2Jenomics Lab Pvt. Ltd. provides a comprehensive bioinformatics workflow for Nanopore Amplicon Sequencing, delivering accurate, publication-ready results from raw sequencing data.

• Standard Analysis

• - High-accuracy basecalling and barcode demultiplexing
• - Read quality assessment and sequencing statistics
• - Species-level taxonomic classification for 16S rRNA and ITS datasets
• - Microbial diversity analysis, including alpha and beta diversity
• - Interactive visualizations such as PCoA and NMDS plots

• Optional Advanced Analysis

• - Differential abundance analysis between sample groups
• - Variant detection for clonal amplicons
• - Consensus sequence generation with error correction
• - Strain-level profiling and fine-scale variant analysis

Example Research Applications

Our Nanopore Amplicon Sequencing service supports a wide range of research applications.

For Research Use Only (RUO). Not intended for clinical or diagnostic applications.

Deliverables

Every project includes comprehensive, analysis-ready datasets.

• • Raw sequencing data (FASTQ and optional FASTA)
• • Quality control reports
• • Taxonomic classification or variant summary tables
• • Relative abundance profiles
• • Publication-ready figures and visualizations
• • Interactive HTML and PDF reports
• • Bioinformatics methods and analysis documentation

Platform Comparison

N2Jenomics Lab Pvt. Ltd. offers sequencing services across multiple technology platforms and helps you select the most appropriate solution for your research.

Our Recommendation

We provide Oxford Nanopore, PacBio, and Illumina sequencing services. Based on your research objectives, sample type, and budget, our scientists will recommend the platform that offers the best balance of accuracy, throughput, turnaround time, and cost.

Sample Requirements

Sample Guidelines

• • DNA should be free of contaminants and degradation.
• • Verify DNA concentration and purity before shipment.
• • Contact our technical team for custom projects or specialized sample requirements.

Why Choose N2Jenomics Lab Pvt. Ltd.?

• Experienced Sequencing Experts

Our team has extensive expertise in Nanopore sequencing and supports a wide range of microbial, genomic, and targeted sequencing applications.

• Advanced Sequencing Technology

We utilize the latest Oxford Nanopore platforms and optimized laboratory workflows to generate reliable, high-quality sequencing data.

• Customized Project Solutions

Every project is tailored to your research goals, ensuring the most appropriate sequencing strategy and bioinformatics analysis.

• Fast Turnaround

Real-time sequencing technology enables rapid project completion without compromising data quality.

• Complete End-to-End Support

From experimental design and sample quality assessment to sequencing, bioinformatics, and final reporting, we provide comprehensive support throughout your project.

1. How does Nanopore Amplicon Sequencing differ from short-read sequencing?

Nanopore sequencing generates full-length amplicon reads, such as complete 16S rRNA and ITS regions, enabling more accurate species- and strain-level identification. In contrast, short-read sequencing analyzes partial gene regions, which may reduce taxonomic resolution.

2. When should barcode-based error correction be used?

Barcode-assisted consensus sequencing is recommended when high accuracy is essential, including:

• • Variant validation in clonal samples

• • Long amplicon sequencing
• • Detection of low-frequency variants or rare microbial species

3. How many sequencing reads are recommended per sample?

The optimal sequencing depth depends on your study design. Microbial community profiling generally requires higher read counts than clonal verification projects. Our team will recommend the appropriate depth based on your research objectives.

4. What factors influence sequencing quality?

High-quality results depend on:

• • Adequate DNA quantity and purity
• • High-integrity DNA samples
• • Specific PCR amplification with minimal non-specific products
• • Proper sample handling and contamination-free preparation

5. What is the typical turnaround time?

Project timelines vary depending on sample type, project complexity, and analysis requirements. Clonal sequencing projects are generally completed more quickly than microbiome or large-scale community profiling studies.

6. Are the results suitable for publication?

Yes. We provide comprehensive, publication-ready reports, quality control metrics, analysis methods, and well-documented bioinformatics results suitable for research publications. This service is intended for Research Use Only (RUO) and is not designed for clinical or diagnostic applications.

7. Which reference databases are used for taxonomic analysis?

We use carefully curated and regularly updated reference databases for full-length 16S rRNA and ITS sequences to improve taxonomic classification and species-level accuracy.

8. Can multiple target genes be sequenced in a single project?

Yes. Multiple amplicon targets can be analyzed provided each PCR product is highly specific. For complex or multiplex projects, our team can recommend the most suitable experimental design to ensure optimal sequencing performance.