MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison.
MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison.
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DOI：
10.1371/journal.pone.0048998
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Ning K
中科院分区：
文献类型：
--
作者：
Song B;Su X;Xu J;Ning K
基于下一代测序（NGS）的宏基因组数据分析正成为微生物群落研究的主流。在宏基因组研究中，面对大量的数据，有效的数据可视化对于科学家有效地探索、解释和处理这些丰富的信息至关重要。宏基因组数据的可视化，特别是多样本数据的可视化，是最关键的挑战之一。不同的数据样本源、排序方法和异构的数据格式使得健壮和无缝的数据可视化变得困难。此外，研究人员对宏基因组研究有不同的关注点：分类或功能，以样本为中心或以基因组为中心，单样本或多样本等，然而，目前在宏基因组数据可视化方面的努力无法满足所有这些需求，并且很难以系统的方式组织所有这些可视化效果。可扩展的交互式可视化工具将是满足所有这些可视化需求的首选方法。在本文中，我们提出了MetaSee，一个可扩展的工具箱，便于交互式可视化的宏基因组样品的利益。MetaSee的主要组成部分包括：（1）一个核心可视化引擎，该引擎由不同的视图组成，用于多个样本的比较：全局视图，系统发育视图，样本视图和分类视图，以及用于更深入分析的链接;（II）具有连接到上述核心可视化引擎的真实的宏基因组模型的前端用户界面，以及（III）用于开发插件的开源门户。在MetaSee。这种一体化的可视化工具不仅提供了可视化效果，而且还使研究人员能够对感兴趣的宏基因组样本进行深入分析。此外，其开源门户允许为MetaSee设计插件，这将有助于开发任何其他可视化效果。
The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.
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影响因子：
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作者：
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通讯作者：
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DOI：
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发表时间：
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期刊：
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影响因子：
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