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ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation

Tom Sante (UGent) , Sarah Vergult (UGent) , Pieter-Jan Volders (UGent) , Wigard P Kloosterman, Geert Trooskens (UGent) , Katleen De Preter (UGent) , Annelies Dheedene (UGent) , Franki Speleman (UGent) , Tim De Meyer (UGent) and Björn Menten (UGent)
(2014) PLOS ONE. 9(12).
Author
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance.
Keywords
REARRANGEMENTS, DATABASE, READ ALIGNMENT, BURROWS-WHEELER TRANSFORM, Data processing, Data visualization, Genome analysis, Genome sequencing, Genomic databases, Genomic libraries, Genomic medicine, Microarrays, SEQUENCES

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Citation

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Chicago
Sante, Tom, Sarah Vergult, Pieter-Jan Volders, Wigard P Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, and Björn Menten. 2014. “ViVar: a Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation.” Plos One 9 (12).
APA
Sante, T., Vergult, S., Volders, P.-J., Kloosterman, W. P., Trooskens, G., De Preter, K., Dheedene, A., et al. (2014). ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLOS ONE, 9(12).
Vancouver
1.
Sante T, Vergult S, Volders P-J, Kloosterman WP, Trooskens G, De Preter K, et al. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLOS ONE. 2014;9(12).
MLA
Sante, Tom, Sarah Vergult, Pieter-Jan Volders, et al. “ViVar: a Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation.” PLOS ONE 9.12 (2014): n. pag. Print.
@article{5782923,
  abstract     = {Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance.},
  articleno    = {e113800},
  author       = {Sante, Tom and Vergult, Sarah and Volders, Pieter-Jan and Kloosterman, Wigard P and Trooskens, Geert and De Preter, Katleen and Dheedene, Annelies and Speleman, Franki and De Meyer, Tim and Menten, Bj{\"o}rn},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {REARRANGEMENTS,DATABASE,READ ALIGNMENT,BURROWS-WHEELER TRANSFORM,Data processing,Data visualization,Genome analysis,Genome sequencing,Genomic databases,Genomic libraries,Genomic medicine,Microarrays,SEQUENCES},
  language     = {eng},
  number       = {12},
  pages        = {12},
  title        = {ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation},
  url          = {http://dx.doi.org/10.1371/journal.pone.0113800},
  volume       = {9},
  year         = {2014},
}

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