Cargando…
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,...
Autores principales: | , , , , , , , , |
---|---|
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 |
_version_ | 1782183328283099136 |
---|---|
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/. |
format | Text |
id | pubmed-2896176 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT houhuabin magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT zhaofangqing magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT zhoulinglin magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT zhuerle magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT tenghuajing magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT lixiaokun magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT baoqiyu magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT wujinyu magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation AT sunzhongsheng magicviewerintegratedsolutionfornextgenerationsequencingdatavisualizationandgeneticvariationdetectionandannotation |