Department of Biological Sciences, University of California, San Diego, San Diego, CA 92093, United States.
Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA 92093, United States.
Bioinformatics. 2023 Sep 2;39(9). doi: 10.1093/bioinformatics/btad538.
Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation.
We present RIVET-a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants and organize the relevant information in a web interface that would help greatly accelerate the process of identifying and tracking recombinants.
RIVET-based web interface displaying the most updated analysis of potential SARS-CoV-2 recombinants is available at https://rivet.ucsd.edu/. RIVET's frontend and backend code is freely available under the MIT license at https://github.com/TurakhiaLab/rivet and the documentation for RIVET is available at https://turakhialab.github.io/rivet/. The inputs necessary for running RIVET's backend workflow for SARS-CoV-2 are available through a public database maintained and updated daily by UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/).
鉴定和追踪 SARS-CoV-2 的重组株对于了解病毒的进化和控制其传播至关重要。但是，从每天在网上共享的数千个新基因组序列中自信地鉴定 SARS-CoV-2 重组株非常具有挑战性，导致许多重组株被遗漏，或者在经过专家整理后，需要数周时间才能被正式鉴定。
我们提出了 RIVET——一个软件管道和可视化平台，它利用了重组推断算法的最新进展，全面而敏感地搜索潜在的 SARS-CoV-2 重组株，并在一个网络界面中组织相关信息，这将极大地加速鉴定和追踪重组株的过程。
基于 RIVET 的网络界面，用于显示潜在 SARS-CoV-2 重组株的最新分析，可在 https://rivet.ucsd.edu/ 上获得。RIVET 的前端和后端代码根据 MIT 许可证在 https://github.com/TurakhiaLab/rivet 上免费提供，RIVET 的文档可在 https://turakhialab.github.io/rivet/ 上获得。运行 RIVET 针对 SARS-CoV-2 的后端工作流程所需的输入可通过 UCSC 维护和每日更新的公共数据库获得（https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/）。
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