Potente Sara, Boscarino Diego, Paladin Dino, Marchini Sergio, Beltrame Luca, Romualdi Chiara
Department of Biology, University of Padova, Via U.Bassi 58/ B, 35131, Italy.
AB Analitica S.r.l., Via Svizzera, 16, 35127, Padova, Italy.
Brief Bioinform. 2024 Nov 22;26(1). doi: 10.1093/bib/bbaf035.
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner. SAMURAI is built using established community standards, ensuring portability, scalability, and reproducibility. The pipeline features a modular design with independent blocks for data preprocessing, copy number analysis, and customized reporting. Users can select workflows tailored for either solid or liquid biopsy analysis (e.g. circulating tumor DNA), with specific tools integrated for each sample type. The final report generated by SAMURAI provides detailed results to facilitate data interpretation and potential downstream analyses. To demonstrate its robustness, SAMURAI was validated using simulated and real-world data sets. The pipeline achieved high concordance with ground truth data and maintained consistent performance across various scenarios. By promoting standardization and offering a versatile workflow, SAMURAI empowers researchers in diverse environments to reliably analyze CNAs from sWGS data. This, in turn, holds promise for advancements in precision medicine.
浅层全基因组测序（sWGS）提供了一种经济高效的方法来检测拷贝数变异（CNA）。然而，专门为sWGS分析设计的标准化工作流程仍存在空白。为满足这一需求，在本研究中我们提出了SAMURAI，这是一种专门设计用于以标准化和可重复方式分析sWGS数据中CNA的生物信息学流程。SAMURAI是使用既定的社区标准构建的，确保了可移植性、可扩展性和可重复性。该流程具有模块化设计，包含用于数据预处理、拷贝数分析和定制报告的独立模块。用户可以选择针对实体活检或液体活检分析（例如循环肿瘤DNA）量身定制的工作流程，并为每种样本类型集成了特定工具。SAMURAI生成的最终报告提供详细结果，以促进数据解释和潜在的下游分析。为证明其稳健性，SAMURAI使用模拟和真实数据集进行了验证。该流程与真实数据高度一致，并在各种情况下保持一致的性能。通过促进标准化并提供通用的工作流程，SAMURAI使不同环境中的研究人员能够可靠地分析sWGS数据中的CNA。这反过来有望推动精准医学的发展。
