EagleView: A genome assembly viewer for next-generation sequencing technologies
EagleView: A genome assembly viewer for next-generation sequencing technologies
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DOI：
10.1101/gr.076067.108
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发表时间：
2008-09-01
期刊：
影响因子：
7
通讯作者：
Marth, Gabor
中科院分区：
文献类型：
--
作者：
Huang, Weichun;Marth, Gabor
高通量下一代测序技术的出现（e.例如，在一个实施例中，454 Life Sciences [Roche]、Illumina测序[前身为Solexa测序]）极大地加快了全基因组从头测序和重测序。虽然这些测序技术的低成本为全基因组多态性发现提供了无与伦比的机会，但新数据类型和巨大数据量的分析对碱基调用，读段比对和基因组组装，多态性检测以及数据可视化提出了巨大的信息学挑战。我们引入了一个新的数据集成和可视化工具MapleView，以方便数据分析，可视化验证和假设生成。RealView可以处理数百万读取的大型基因组组装。它支持紧凑的装配视图、多种导航模式和特定于技术的跟踪信息的精确视图。此外，MapleView支持查看来自不同技术的混合类型读段的共组装，并支持将基因组特征注释整合到基因组组装中。我们自己的实验室和全球100多个研究实验室都使用了RealView进行下一代序列分析。在www.example.com上可以免费获得非盈利性软件。http://bioinformatics.bc.edu/marthlab/EagleView
The emergence of high-throughput next-generation sequencing technologies (e. g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo sequencing and resequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome assembly, polymorphism detection, as well as data visualization. We introduce a new data integration and visualization tool EagleView to facilitate data analyses, visual validation, and hypothesis generation. EagleView can handle a large genome assembly of millions of reads. It supports a compact assembly view, multiple navigation modes, and a pinpoint view of technology-specific trace information. Moreover, EagleView supports viewing coassembly of mixed-type reads from different technologies and supports integrating genome feature annotations into genome assemblies. EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView.