Huang Weichun, Marth Gabor
Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA.
Genome Res. 2008 Sep;18(9):1538-43. doi: 10.1101/gr.076067.108. Epub 2008 Jun 11.
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.
高通量新一代测序技术（例如454生命科学公司[罗氏公司]、Illumina测序技术[原Solexa测序技术]）的出现极大地加速了全基因组从头测序和重测序的进程。尽管这些测序技术成本低廉，为全基因组多态性发现提供了前所未有的机遇，但对新数据类型和海量数据的分析在碱基识别、读段比对与基因组组装、多态性检测以及数据可视化等方面带来了巨大的信息学挑战。我们推出了一种新的数据整合与可视化工具EagleView，以促进数据分析、可视化验证和假设生成。EagleView能够处理包含数百万条读段的大型基因组组装。它支持紧凑的组装视图、多种导航模式以及特定技术的痕量信息的精确视图。此外，EagleView支持查看来自不同技术的混合型读段的共组装，并支持将基因组特征注释整合到基因组组装中。EagleView已在我们自己的实验室以及全球超过100个研究实验室中用于新一代序列分析。EagleView软件可在http://bioinformatics.bc.edu/marthlab/EagleView免费获取，供非商业用途使用。
