GfaViz: flexible and interactive visualization of GFA sequence graphs
GfaViz: flexible and interactive visualization of GFA sequence graphs
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DOI：
10.1093/bioinformatics/bty1046
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发表时间：
2019-08-15
期刊：
影响因子：
5.8
通讯作者：
Kurtz, Stefan
中科院分区：
文献类型：
--
作者：
Gonnella, Giorgio;Niehus, Niklas;Kurtz, Stefan
摘要：图形片段组装（GFA）格式是用于表示序列图的新兴标准格式。虽然GFA 1主要针对组装图，但较新的GFA 2格式引入了几个功能，这使得它适合表示其他类型的信息，例如支架图，变异图，对齐图和彩色宏基因组图。在这里，我们提出了GfaViz，一个交互式的图形工具，用于GFA格式的序列图的可视化。该软件支持GFA 2的所有新功能，并为其可视化引入了约定。用户可以选择两种不同的布局和多种样式来表示单个元素或组。所有定制都可以存储在GFA格式的自定义标记中，而不需要外部配置文件。支持样式表来存储文件组的标准配置选项。可视化可以导出为光栅和矢量图形格式。命令行界面允许批量生成图像。
A Summary: The graphical fragment assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. Although GFA 1 was primarily targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images.