N2Jenomics Lab Pvt. Ltd. offers Long Amplicon Analysis (LAA) using PacBio SMRT sequencing, delivering high-accuracy sequencing for amplicons ranging from a few hundred base pairs up to 10 kb. Flexible sequencing depths (<500 to 10,000 CCS reads per sample) are available to meet diverse research needs.

What Is Long Amplicon Analysis?

Long Amplicon Analysis (LAA) is a long-read sequencing approach for analyzing extended DNA fragments with exceptional accuracy. Using PacBio Circular Consensus Sequencing (CCS), the same DNA molecule is sequenced multiple times to generate highly accurate long reads with >99.9% accuracy.

LAA enables direct analysis of long PCR amplicons without complex assembly, making it ideal for detecting genetic variants, resolving complex genomic regions, and reconstructing haplotypes.

Key Advantages

• • High Sequencing Accuracy with PacBio HiFi CCS reads (>99.9% accuracy).

• • Long-Read Coverage for amplicons up to 10 kb.
• • Resolves Complex Genomic Regions, including repetitive sequences.
• • Sensitive Variant Detection for SNPs, InDels, CNVs, and structural variants.
• • Accurate Haplotype Phasing within individual amplicons.
• • Full-Length Gene Coverage to capture complete gene sequences and mutations.
• • Simplified Data Analysis with minimal assembly requirements.

Applications

• • Full-Length 16S/18S/ITS Amplicon Sequencing
• • High-Resolution HLA Typing
• • Haplotype Analysis and Phasing
• • Targeted de novo Gene Assembly
• • Custom Long Amplicon Sequencing
• • Targeted Variant Detection
• • Disease and Genetic Research

Long Amplicon Analysis Workflow

Service Specification

	Sample Requirements 2 µg or more of amplicons (i.e. purified PCR Products) with a concentration of ~50ng/µl or higher, be dissolved in Tris-HCl buffer (10 mM, pH 8) and shipped on dry ice packs. We also provide amplicon preparation service, from starting materials including genomic DNA, cell pellets, and tissues.
	Sequencing PacBio sequencing platform 3 kb to >10 kb amplicons >99.999% accuracy
	Bioinformatics Analysis For full-length 16S/18S/ITS gene sequencing: OTUs clustering and filtering OTUs analysis and species annotation Alpha diversity, Beta diversity, Meta-analysis Multi-variate statistical analysis For other applications, please inquire.

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in Long Amplicon Analysis for your writing (customization)

1. What are the major applications of Long Amplicon Analysis?

Long Amplicon Analysis is widely used for:

• • Structural variant analysis (insertions, deletions, inversions, and repeat regions)
• • Genetic disease research involving large or complex genomic variants
• • Evolutionary and phylogenetic studies
• • Microbial diversity and community profiling
• • Targeted gene sequencing and haplotype analysis

2. What is the workflow for Long Amplicon Analysis?

A typical LAA workflow includes:

• High-quality DNA extraction

• Long-range PCR amplification using high-fidelity polymerases

• Amplicon purification

• Library preparation and quality assessment

• Long-read sequencing (PacBio or Oxford Nanopore)

• Bioinformatics analysis, including quality control, alignment, variant detection, and annotation

• Validation and delivery of results

3. Which bioinformatics analyses are included?

LAA data analysis typically includes:

• • Raw data quality assessment
• • Read alignment and genome assembly
• • SNP, InDel, and structural variant detection
• • Functional annotation
• • Haplotype analysis (when applicable)
• • Comprehensive quality reports

4. How is data accuracy ensured?

High-quality results are achieved through:

• • High-integrity DNA samples
• • Optimized long-range PCR conditions
• • High-fidelity DNA polymerases
• • Stringent quality control during library preparation and sequencing
• • Advanced bioinformatics pipelines
• • Optional validation using methods such as Sanger sequencing or qPCR for critical findings.