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Sante T, Vergult S, Volders PJ, et al. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One. 2014;9(12):e113800doi: 10.1371/journal.pone.0113800.
Sante, T., Vergult, S., Volders, P. J., Kloosterman, W. P., Trooskens, G., De Preter, K., Dheedene, A., Speleman, F., De Meyer, T., & Menten, B. (2014). ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PloS one, 9(12), e113800. https://doi.org/10.1371/journal.pone.0113800
Sante, Tom, et al. "ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation." PloS one vol. 9,12 (2014): e113800. doi: https://doi.org/10.1371/journal.pone.0113800
Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One. 2014 Dec 12;9(12):e113800. doi: 10.1371/journal.pone.0113800. eCollection 2014. PMID: 25503062; PMCID: PMC4264741.
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PLoS One. 2014 Dec 12;9(12):e113800. doi: 10.1371/journal.pone.0113800. eCollection 2014.

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

PloS one

Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Frank Speleman, Tim De Meyer, Björn Menten

Affiliations

  1. Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium.
  2. Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
  3. BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.

PMID: 25503062 PMCID: PMC4264741 DOI: 10.1371/journal.pone.0113800

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. URL: https://www.cmgg.be/vivar/

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