COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists
COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists
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DOI：
10.1089/omi.2013.0119
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发表时间：
2014-03-01
影响因子：
3.3
通讯作者：
Dupuy, Bruno
中科院分区：
文献类型：
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作者：
Monot, Marc;Orgeur, Mickael;Dupuy, Bruno
COV2HTML是一个面向生物学家的交互式网络界面，允许对原核生物(细菌和噬菌体)进行覆盖可视化和NGS比对分析。它结合了两个过程：一个工具，将巨大的NGS地图或覆盖范围文件转换为包含遗传要素信息的特定于光的覆盖范围文件；以及一个可视化界面，允许实时分析数据，并可选择整合统计结果。为了演示COV2HTML的范围，用两个已发表的研究中的数据对该程序进行了测试。第一个数据来自空肠弯曲菌的RNA-seq分析，基于两个条件和两个重复的比较。使用COV2HTML，我们能够恢复该出版物中突出显示的27个基因中的26个。第二个数据由Archaea Sulfolobus solfararicus上的TSS和RNA-seq数据集组成。COV2HTML能够突出显示文章中的大多数TSS，并允许生物学家在同一屏幕上可视化TSS和RNA-seq。COV2HTML界面的强大之处在于使NGS数据分析成为可能，而无需安装软件、登录或长时间培训。网页版本可在https://mmonot.eu/COV2HTML/.上访问这个网站是免费的，对用户开放，无需任何登录要求。
COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/. This website is free and open to users without any login requirement.