Back to top

Nanopore (ONT) AAV Genome Sequencing

 
 
Unlock full-length AAV genomes from intact capsids — fast and efficient.
Detect subgenomic variants, assess integrity, and reveal structural configurations that short-read methods may miss.

What You Can Achieve

  • Detect subgenomic variants such as truncated, inverted, or snapback genomes (SBG)
  • Generate full-length consensus sequences from native rAAV DNA
  • Preserve intact ITRs and native genome structures without PCR artifacts
  • Assess structural integrity and heterogeneity of vector preparations
  • Receive interactive genome maps and quantitative metrics on genome composition

Before You Start

To optimize your project, please clarify:

  • What is the sample input (vector genome copies and purification method)?
  • Is your focus on structural integrity, variant detection, or both?
  • Do you require raw reads for your own downstream analysis?

Workflow

A minimal-hands-on workflow designed to preserve native AAV structures:

Oxford Nanopore AAV Genome Sequencing

Bioinformatics Analysis

Our specialized pipeline reconstructs native and subgenomic species:

  • High-accuracy consensus of full-length and subgenomic genomes
  • Detection of truncations, deletions, and analysis of structural integrity
  • ITR orientation (flip-flop) configuration analysis
  • Quantitative breakdown of all genome subspecies
  • Read-level visualizations of structural composition

You receive:

  • FASTA consensus sequences
  • Interactive genome map
  • Variant abundance table
  • ITR orientation summary
  • Truncation analysis
  • Read length histogram & quality analysis
  • Optional: raw reads

Turnaround Time

  • 1 week or less from sample receipt to report
  • Includes sequencing and full de novo analysis

Sample Requirements

Input Amount

  • Minimum: 1.0 × 10¹¹ vector genomes (VG) per sample
  • Recommended: 2–5 × 10¹¹ VG per sample
  • Volume: Up to 200 μl in buffered saline or AAV-compatible buffer

Purity

  • Must be free of cellular debris
  • Preferably purified by affinity resin or ultracentrifugation
  • Crude PEG-precipitated samples accepted if ≥2 × 10¹¹ VG