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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences
PloS one, v 12(8), pp e0182843-e0182843
2017
PMID: 28829778
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.
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Details
- Title
- ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences
- Creators
- Fwu-Shan Shieh - JBS SciencePatrick Jongeneel - JBS ScienceJamin D Steffen - JBS ScienceSelena Lin - U-Screen Dx Inc., Doylestown, Pennsylvania, United States of America.Surbhi Jain - JBS ScienceWei Song - JBS Science (United States)Ying-Hsiu Su - Drexel University
- Publication Details
- PloS one, v 12(8), pp e0182843-e0182843
- Publisher
- Public LIbrary of Science (PLOS)
- Grant note
- R44 CA165312 / NCI NIH HHS R01 CA202769 / NCI NIH HHS R43 CA192507 / NCI NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology; A.J. Drexel Autism Institute
- Web of Science ID
- WOS:000408085100018
- Scopus ID
- 2-s2.0-85027852839
- Other Identifier
- 991019167318704721
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- Web of Science research areas
- Multidisciplinary Sciences