Labs, Persistent Systems Limited, Pingala - Aryabhata, Erandwane, Pune, 411004, India.
Present address: Bioinformatics Center, Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India.
BMC Genomics. 2017 Oct 24;18(1):823. doi: 10.1186/s12864-017-4169-5.
Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along with user defined karyotypes. Circular plot provides holistic visualization of high throughput large scale data but it is very complex and challenging to generate as most of the available tools need informatics expertise to install and run them.
We have developed CGDV (Circos for Genomics and Transcriptomics Data Visualization), a webtool based on Circos, for seamless and automated visualization of a variety of large scale genomics and transcriptomics data. CGDV takes output of analyzed genomics or transcriptomics data of different formats, such as vcf, bed, xls, tab limited matrix text file, CNVnator raw output and Gene fusion raw output, to plot circular view of the sample data. CGDV take cares of generating intermediate files required for circos. CGDV is freely available at https://cgdv-upload.persistent.co.in/cgdv/ .
The circular plot for each data type is tailored to gain best biological insights into the data. The inter-relationship between data points, homologous sequences, genes involved in fusion events, differential expression pattern, sequencing depth, types and size of variations and enrichment of DNA binding proteins can be seen using CGDV. CGDV thus helps biologists and bioinformaticians to visualize a variety of genomics and transcriptomics data seamlessly.
大规模数据的解读极具挑战性，目前缺乏支持自动化可视化各种高通量基因组学和转录组学数据的网络工具，也无法针对各种模式生物以及用户定义的核型进行可视化。环形图提供了高通量大数据的整体可视化，但由于大多数可用工具需要计算专业知识来安装和运行，因此生成它非常复杂且具有挑战性。
我们开发了 CGDV（基于 Circos 的基因组学和转录组学数据可视化工具），这是一个基于 Circos 的网络工具，用于无缝和自动化地可视化各种大规模基因组学和转录组学数据。CGDV 接受不同格式的分析基因组学或转录组学数据的输出，例如 vcf、bed、xls、制表符限制矩阵文本文件、CNVnator 原始输出和基因融合原始输出，以绘制样本数据的环形视图。CGDV 负责生成 Circos 所需的中间文件。CGDV 可在 https://cgdv-upload.persistent.co.in/cgdv/ 免费获得。
针对每种数据类型的环形图都经过精心设计，以最大程度地深入了解数据的生物学特性。使用 CGDV 可以看到数据点、同源序列、融合事件中涉及的基因、差异表达模式、测序深度、变异的类型和大小以及 DNA 结合蛋白的富集之间的相互关系。因此，CGDV 有助于生物学家和生物信息学家无缝地可视化各种基因组学和转录组学数据。
