Second, viral taxonomies based on the International Committee on Taxonomy of Viruses (ICTV) are subject to new revisions. This is compounded by disparate, open-source tools which are often command-line based and require advanced computational or coding skills. First, the enormous amounts of complex data generated from each sample is non-trivial. However, bioinformatics analysis remains a bottleneck. The wet lab portion of genomics research has become more streamlined, simpler, and accessible to the researcher. Since the commercialization of high-throughput sequencing (HTS) instruments in 2005, the variety and choices of sequencing technologies, chemistries, platforms, capacities, and kits have expanded exponentially. Recent advancements in next-generation sequencing (NGS) have actualized HPV virome profiling. The entire process named “HPV DeepSeq” provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Tabular output conversion to visualizations entailed 1–2 keystrokes. Low-grade ( n = 95) and high-grade ( n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min) Alpha/Beta Diversities (5 s) Map Reads (45 min). HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC “ready-to-use” workflows for stepwise data processing to include: (1) Taxonomic Analysis, (2) Estimate Alpha/Beta Diversities, and (3) Map Reads to Reference. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized papillomavirus database in the CLC Microbial Genomics Module. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis.
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