Park Byeonghyeok, Baek Min-Jeong, Min Byoungnam, Choi In-Geol
Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University , Seoul, Korea.
J Comput Biol. 2017 Sep;24(9):917-922. doi: 10.1089/cmb.2017.0066. Epub 2017 Jun 20.
Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.
基因组注释是基因组研究的首要步骤。为了建立一个轻便且适用于单个实验室的原核生物基因组注释流程，我们开发了一个名为“P-CAPS”（原核生物重叠群注释流程服务器）的Shiny应用程序包。该程序包由R和Python脚本组成，这些脚本将公开可用的注释程序集成到一个服务器应用程序中。P-CAPS不仅是一个基于浏览器的交互式应用程序，还是一个可分发的Shiny应用程序包，可以安装在任何个人计算机上。最终注释以各种标准格式提供，并汇总在一个R markdown文档中。注释可以通过公共基因组浏览器进行可视化和检查。一项基准测试表明，P-CAPS的注释质量和完整性是可靠的，并且与当前可用的公共流程兼容。
