AAV Genome Sequencing
The DNA Core now offers a cost-effective, high-resolution solution for direct sequencing and quality control of full-length recombinant adeno-associated virus (rAAV) vectors using Oxford Nanopore long-read sequencing technology. This comprehensive service includes extraction of intact viral genomes from purified AAV capsids, library preparation with Oxford Nanopore's latest V14 chemistry, and sequencing on R10.4.1 flow cells.
Automated analysis based on Oxford Nanopore's EPI2ME AAV workflow provides in-depth validation of rAAV vectors including resolution of inverted terminal repeats (ITRs), detection of mutations, structural variants, contaminants, as well as identification of truncation hotspots. Reads are classified into AAV subgenome types- including full-length, partial, rearranged, or plasmid-derived- offering detailed insight into packaging fidelity and vector heterogeneity.
Results include an interactive HTML report along with FASTA, BAM, VCF, and summary tables to support full vector assessment- ideal for research, production, and preclinical validation. Click here for a more detailed explanation of our pipeline and descriptions of delivered data files.
rAAV sequencing at the CCIB DNA Core is for research purposes only and not for clinical use.
At present, our analysis pipeline can only process single-stranded rAAV (ssAAV). Please contact us if you require self-complementary rAAV sequencing!
Samples submitted by Tuesday at 12:00 PM will have data delivered by end of the day on Friday .
Service Features
- Fast turnaround
- Cost-effective
- Affordable, high-quality sequencing and analysis
- Comprehensive AAV QC reporting
- Full Vector Validation
- Detection of Truncation Hotspots
- Genome Coverage and ITR Resolution
- AAV Subgenome Metrics
- Interactive HTML Report
Delivered Data Files
- Raw FASTQ reads
- Quality report of FASTQ reads
- Polished consensus FASTA of full-length AAV genome
- VCF identifying sequence differences between the reference transgene plasmid FASTA and the Nanopore-derived polished consensus FASTA
- Interactive HTML report with read quality, contamination, truncation, ITR-to-ITR coverage, and AAV subgenome classification plots
- TSV detailing per read subgenome type
- BAM/BAI files of reads aligned to the reference files with a TSV of alignment statistics (e.g., mapping quality, read coverage)
For detailed sample preparation and submission requirements, please visit our Sample Submission Guidelines.
Please contact us to discuss your specific project needs.