Interest in gene therapy-based disease prevention and treatment has grown rapidly over the last decade. While lentivirus has been the viral vector of choice for gene therapy, recombinant adeno-associated viral (rAAV) vectors have seen recent widespread application due to the non-integrating ability. Baculoviruses are emerging as a highly adaptable vector with a broad tissue and host tropism. Regardless of vector, extensive quality control (QC) throughout the entire development and manufacturing process is essential. A robust QC process expedites safe, effective commercialization of final product. While Sanger sequencing can be ideal to verify and validate sequences pre-packaging, next generation sequencing (NGS) combined with post-viral production methodologies like CE analysis and transmission electron microscopy offer an effective high-throughput approach for monitoring quality, from initial construct assembly to analysis of the encapsulated product. Both short-read and long-read sequencing technologies offer distinct advantages including sequencing of the entire viral genome, with detection of potential mutations, truncations, and contaminants. Here we describe our novel proprietary vector-agnostic workflows, for use in lentiviral, AAV or baculovirus settings. Starting with high quality synthesis of either vector plasmid or region of interest, full-length plasmid sequence is confirmed. Depending on these results, correction or new synthesis of plasmid options are applied. Following packaging within the viral vector system of choice, QC results using both short- and long-read NGS platforms are supported with a regulatory-compliant Sanger assay. State of the art synthesis reduces potential upstream errors. Sanger ITR sequencing and sequence correction upstream alleviates potential downstream issues in viral packaging. High-quality viral packaging ensures robust viral titers for downstream use. The combined NGS approach post-packaging alleviates current constraints for high throughput AAV sequencing and thereby enhance the overall QC process. Our Good Laboratory Practices (GLP) Sanger sequencing method extends read lengths through the entire ITR regions, allowing for rapid sequence confirmation of the final AAV product. The combination of these approaches enables a comprehensive solution, ideal for sequence confirmation of both transfer plasmid and final packaged product for improved viral vector gene therapy manufacturing in advance of FDA or EMA filings.