标题： AMRScan：一种混合R和Nextflow工具包，用于从测序数据中快速检测抗菌素耐药基因 显示英文标题

标题： AMRScan: A hybrid R and Nextflow toolkit for rapid antimicrobial resistance gene detection from sequencing data

摘要： AMRScan是一个混合生物信息学工具包，用R和[Nextflow](https://www.nextflow.io/)实现，用于从下一代测序(NGS)数据中快速且可重复地检测抗菌药物耐药(AMR)基因。该工具包使用户能够通过将测序读数与参考数据库如CARD进行BLAST比对来识别AMR基因命中。R实现提供了一种简洁的基于脚本的方法，适用于单样本分析、教学和快速原型设计。相比之下，Nextflow实现能够在高性能计算(HPC)和容器化环境中为多样本批量处理提供可重复且可扩展的工作流程。它利用模块化管道设计，支持自动数据库设置、质量控制、转换、BLAST比对和结果解析。AMRScan有助于弥合轻量级探索性分析与生产就绪的监测管道之间的差距，使其适用于研究和公共卫生基因组学应用。 显示英文摘要

摘要： AMRScan is a hybrid bioinformatics toolkit implemented in both R and [Nextflow](https://www.nextflow.io/) for the rapid and reproducible detection of antimicrobial resistance (AMR) genes from next-generation sequencing (NGS) data. The toolkit enables users to identify AMR gene hits in sequencing reads by aligning them against reference databases such as CARD using BLAST. The R implementation provides a concise, script-based approach suitable for single-sample analysis, teaching, and rapid prototyping. In contrast, the Nextflow implementation enables reproducible, scalable workflows for multi-sample batch processing in high-performance computing (HPC) and containerized environments. It leverages modular pipeline design with support for automated database setup, quality control, conversion, BLAST alignment, and results parsing. AMRScan helps bridge the gap between lightweight exploratory analysis and production-ready surveillance pipelines, making it suitable for both research and public health genomics applications.