Open Access
ARTICLE
Viral integration detection strategies and a technical update on Virus-Clip
DANIEL WAI-HUNG HO1,2,#, XUEYING LYU1,2,#, IRENE OI-LIN NG1,2,*
1 Department of Pathology, The University of Hong Kong, Hong Kong, China
2 State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, China
* Corresponding Author: Irene Oi-lin Ng,
# Authors contributed equally to this study
BIOCELL 2021, 45(6), 1495-1500. https://doi.org/10.32604/biocell.2021.017227
Received 23 April 2021; Accepted 31 May 2021; Issue published 01 September 2021
Abstract
Oncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in
the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration
detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration
phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we
provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38)
and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of Virus-Clip
using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated
hepatocellular carcinoma patients, we demonstrate the marked improvement of multi-thread mode in terms of
significantly reduced execution time, while there is negligible difference in memory usage. Taken together, with the
current update of Virus-Clip, it will continue supporting the
in silico detection of oncoviral integration for better
understanding of various human malignancies.
Keywords
Cite This Article
APA Style
HO, D.W., LYU, X., NG, I.O. (2021). Viral integration detection strategies and a technical update on virus-clip. BIOCELL, 45(6), 1495-1500. https://doi.org/10.32604/biocell.2021.017227
Vancouver Style
HO DW, LYU X, NG IO. Viral integration detection strategies and a technical update on virus-clip. BIOCELL . 2021;45(6):1495-1500 https://doi.org/10.32604/biocell.2021.017227
IEEE Style
D.W. HO, X. LYU, and I.O. NG "Viral integration detection strategies and a technical update on Virus-Clip," BIOCELL , vol. 45, no. 6, pp. 1495-1500. 2021. https://doi.org/10.32604/biocell.2021.017227