HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench
| dc.contributor.author | Shen-Gunther, Jane | |
| dc.contributor.author | Xia, Qingqing | |
| dc.contributor.author | Cai, Hong | |
| dc.contributor.author | Wang, Yufeng | |
| dc.date.accessioned | 2021-08-26T13:28:26Z | |
| dc.date.available | 2021-08-26T13:28:26Z | |
| dc.date.issued | 2021-08-13 | |
| dc.date.updated | 2021-08-26T13:28:27Z | |
| dc.description.abstract | Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. 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. 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. 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). Tabular output conversion to visualizations entailed 1–2 keystrokes. 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. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of 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. | |
| dc.description.department | Molecular Microbiology and Immunology | |
| dc.identifier | doi: 10.3390/pathogens10081026 | |
| dc.identifier.citation | Pathogens 10 (8): 1026 (2021) | |
| dc.identifier.uri | https://hdl.handle.net/20.500.12588/672 | |
| dc.rights | Attribution 4.0 United States | |
| dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
| dc.subject | bioinformatics | |
| dc.subject | cervical cancer | |
| dc.subject | deep sequencing | |
| dc.subject | human papillomavirus | |
| dc.subject | HPV genotyping | |
| dc.subject | metagenome | |
| dc.subject | next generation sequencing | |
| dc.subject | taxonomic classification | |
| dc.subject | virome | |
| dc.title | HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench | |
| dc.type | Article |