title: Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability.
abstract: Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku.hk/~dwhho/Virus-Clip.zip.
authors.affiliation: Department of Pathology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
authors.forename: Daniel W H
authors.initials: DW
authors.lastname: Ho
authors.affiliation: Department of Pathology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
authors.forename: Karen M F
authors.initials: KM
authors.lastname: Sze
authors.affiliation: Department of Pathology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
authors.forename: Irene O L
authors.initials: IO
authors.lastname: Ng
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000821:virology*; D019295:Computational Biology / Q000379:methods*; D015894:Genome, Human; D006509:Hepatitis B / Q000821:virology; D006515:Hepatitis B virus / Q000378:metabolism; D006801:Humans; D008113:Liver Neoplasms / Q000821:virology*; D016133:Polymerase Chain Reaction; D011381:Programming Languages; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome; D016662:Virus Integration; D014780:Viruses / Q000378:metabolism*
keywords: breakpoint detection; next-generation sequencing; viral integration; viral integration site detection