Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

被引：0
|
作者：
Atul Kamboj
Claus V. Hallwirth
Ian E. Alexander
Geoffrey B. McCowage
Belinda Kramer
机构：
[1] Kids’ Research Institute,Children’s Cancer Research Unit
[2] The Children’s Hospital at Westmead,Gene Therapy Research Unit
[3] Children’s Medical Research Institute and The Children’s Hospital at Westmead,The University of Sydney
[4] Discipline of Paediatrics and Child Health,Cancer Centre for Children
[5] The Children’s Hospital,undefined
来源：
BMC Bioinformatics | / 18卷
关键词：
Gene therapy; Integration site analysis; Next-generation sequencing; Viral vectors;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
引用
收藏
相关论文
共 43 条
  • [31] AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data
    Ghorbani, Abozar
    Rostami, Mahsa
    Guzzi, Pietro Hiram
    FRONTIERS IN GENETICS, 2024, 15
  • [32] A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data
    O'Fallon, Brendan D.
    Wooderchak-Donahue, Whitney
    Crockett, David K.
    BIOINFORMATICS, 2013, 29 (11) : 1361 - 1366
  • [33] HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data
    Baheti, Saurabh
    Tang, Xiaojia
    O'Brien, Daniel R.
    Chia, Nicholas
    Roberts, Lewis R.
    Nelson, Heidi
    Boughey, Judy C.
    Wang, Liewei
    Goetz, Matthew P.
    Kocher, Jean-Pierre A.
    Kalari, Krishna R.
    BMC BIOINFORMATICS, 2018, 19
  • [34] HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data
    Saurabh Baheti
    Xiaojia Tang
    Daniel R. O’Brien
    Nicholas Chia
    Lewis R. Roberts
    Heidi Nelson
    Judy C. Boughey
    Liewei Wang
    Matthew P. Goetz
    Jean-Pierre A. Kocher
    Krishna R. Kalari
    BMC Bioinformatics, 19
  • [35] Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data
    Stephens, Zachary
    O'Brien, Daniel
    Dehankar, Mrunal
    Roberts, Lewis R.
    Iyer, Ravishankar K.
    Kocher, Jean-Pierre
    PLOS ONE, 2021, 16 (09):
  • [36] Concod: an effective integration framework of consensus-based calling deletions from next-generation sequencing data
    Cai, Lei
    Chu, Chong
    Zhang, Xiaodong
    Wu, Yufeng
    Gao, Jingyang
    INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS, 2017, 17 (02) : 153 - 172
  • [37] Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data
    Cheng, Ji-Hong
    Liu, Wen-Chun
    Chang, Ting-Tsung
    Hsieh, Sun-Yuan
    Tseng, Vincent S.
    METHODS, 2017, 129 : 24 - 32
  • [38] A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity
    Gong, Yu-Nong
    Chen, Guang-Wu
    Yang, Shu-Li
    Lee, Ching-Ju
    Shih, Shin-Ru
    Tsao, Kuo-Chien
    PLOS ONE, 2016, 11 (03):
  • [39] A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections
    Bovo, Samuele
    Mazzoni, Gianluca
    Ribani, Anisa
    Utzeri, Valerio Joe
    Bertolini, Francesca
    Schiavo, Giuseppina
    Fontanesi, Luca
    PLOS ONE, 2017, 12 (06):
  • [40] INTEGRATION OF GENOMIC DATA FROM THE ONCOKIDSSM NEXT GENERATION SEQUENCING PANEL AND CHROMOSOMAL MICROARRAY ANALYSIS FOR DIAGNOSIS AND PROGNOSIS OF PEDIATRIC CNS TUMORS
    Kaneva, Kristiyana
    Hiemenz, Matthew
    Ji, Jianling
    Robison, Nathan
    Margol, Ashley
    Dhall, Girish
    Cotter, Jennifer
    Hawes, Debra
    Judkins, Alexander
    Biegel, Jaclyn A.
    NEURO-ONCOLOGY, 2018, 20 : 181 - 181
12345