High-throughput DNA and RNA sequencing are revolutionizing precision oncology, enabling personalized therapies such as cancer vaccines designed to target tumor-specific neoepitopes generated by somatic mutations expressed in cancer cells. Identification of these neoepitopes from next-generation sequencing data of clinical samples remains challenging and requires the use of complex bioinformatics pipelines. In this paper, we present GeNeo, a bioinformatics toolbox for genomics-guided neoepitope prediction. GeNeo includes a comprehensive set of tools for somatic variant calling and filtering, variant validation, and neoepitope prediction and filtering. For ease of use, GeNeo tools can be accessed via web-based interfaces deployed on a Galaxy portal publicly accessible at https://neo.engr.uconn.edu/. A virtual machine image for running GeNeo locally is also available to academic users upon request.

中文翻译：

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GeNeo：用于基因组学指导的新表位预测的生物信息学工具箱。

高通量 DNA 和 RNA 测序正在彻底改变精准肿瘤学，使个性化疗法成为可能，例如癌症疫苗旨在靶向癌细胞中表达的体细胞突变产生的肿瘤特异性新表位。从临床样本的下一代测序数据中鉴定这些新表位仍然具有挑战性，需要使用复杂的生物信息学流程。在本文中，我们介绍了 GeNeo，这是一种用于基因组学指导的新表位预测的生物信息学工具箱。GeNeo 包括一套全面的工具，用于体细胞变异检出和过滤、变异验证以及新表位预测和过滤。为便于使用，GeNeo 工具可通过部署在 Galaxy 门户网站上的基于 Web 的界面访问，可在 https://neo.engr.uconn.edu/ 上公开访问。