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MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

New sequencing technologies, such as Roche 454, ABI SOLiD and Illumina, have been increasingly developed at an astounding pace with the advantages of high throughput, reduced time and cost. To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing,...

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Detalles Bibliográficos
Autores principales: Hou, Huabin, Zhao, Fangqing, Zhou, LingLin, Zhu, Erle, Teng, Huajing, Li, Xiaokun, Bao, Qiyu, Wu, Jinyu, Sun, Zhongsheng
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896176/
https://www.ncbi.nlm.nih.gov/pubmed/20444865
http://dx.doi.org/10.1093/nar/gkq302
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author Hou, Huabin
Zhao, Fangqing
Zhou, LingLin
Zhu, Erle
Teng, Huajing
Li, Xiaokun
Bao, Qiyu
Wu, Jinyu
Sun, Zhongsheng
author_facet Hou, Huabin
Zhao, Fangqing
Zhou, LingLin
Zhu, Erle
Teng, Huajing
Li, Xiaokun
Bao, Qiyu
Wu, Jinyu
Sun, Zhongsheng
author_sort Hou, Huabin
collection PubMed
description New sequencing technologies, such as Roche 454, ABI SOLiD and Illumina, have been increasingly developed at an astounding pace with the advantages of high throughput, reduced time and cost. To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, an integrated software MagicViewer is developed to easily visualize short read mapping, identify and annotate genetic variation based on the reference genome. MagicViewer provides a user-friendly environment in which large-scale short reads can be displayed in a zoomable interface under user-defined color scheme through an operating system-independent manner. Meanwhile, it also holds a versatile computational pipeline for genetic variation detection, filtration, annotation and visualization, providing details of search option, functional classification, subset selection, sequence association and primer design. In conclusion, MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data, which can be widely used in a variety of sequencing-based researches, including genome re-sequencing and transcriptome studies. MagicViewer is freely available at http://bioinformatics.zj.cn/magicviewer/.
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spelling pubmed-28961762010-07-02 MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation Hou, Huabin Zhao, Fangqing Zhou, LingLin Zhu, Erle Teng, Huajing Li, Xiaokun Bao, Qiyu Wu, Jinyu Sun, Zhongsheng Nucleic Acids Res Stand-Alone Programs for High-Throughput Data New sequencing technologies, such as Roche 454, ABI SOLiD and Illumina, have been increasingly developed at an astounding pace with the advantages of high throughput, reduced time and cost. To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, an integrated software MagicViewer is developed to easily visualize short read mapping, identify and annotate genetic variation based on the reference genome. MagicViewer provides a user-friendly environment in which large-scale short reads can be displayed in a zoomable interface under user-defined color scheme through an operating system-independent manner. Meanwhile, it also holds a versatile computational pipeline for genetic variation detection, filtration, annotation and visualization, providing details of search option, functional classification, subset selection, sequence association and primer design. In conclusion, MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data, which can be widely used in a variety of sequencing-based researches, including genome re-sequencing and transcriptome studies. MagicViewer is freely available at http://bioinformatics.zj.cn/magicviewer/. Oxford University Press 2010-07-01 2010-05-05 /pmc/articles/PMC2896176/ /pubmed/20444865 http://dx.doi.org/10.1093/nar/gkq302 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Stand-Alone Programs for High-Throughput Data
Hou, Huabin
Zhao, Fangqing
Zhou, LingLin
Zhu, Erle
Teng, Huajing
Li, Xiaokun
Bao, Qiyu
Wu, Jinyu
Sun, Zhongsheng
MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title_full MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title_fullStr MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title_full_unstemmed MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title_short MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
title_sort magicviewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
topic Stand-Alone Programs for High-Throughput Data
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896176/
https://www.ncbi.nlm.nih.gov/pubmed/20444865
http://dx.doi.org/10.1093/nar/gkq302
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