AMRScan：一个用 R 和 Nextflow 实现的混合工具包，用于从测序数据中快速检测抗菌素耐药基因
AMRScan 2: provenance-recorded detection of antimicrobial resistance determinants in bacterial assemblies, with archived susceptibility data from NCBI Pathogen Detection
AI总结：
AMRScan 是一个用 R 和 Nextflow 实现的混合生物信息学工具包，通过 BLAST 比对参考数据库，支持从 NGS 数据中快速、可重复地检测抗菌素耐药基因，兼顾单样本分析与多样本批量处理。
摘要：
AMRScan 是一个用 R 和 Nextflow 实现的混合生物信息学工具包，用于从下一代测序（NGS）数据中快速、可重复地检测抗菌素耐药（AMR）基因。该工具包允许用户通过使用 BLAST 将测序读段与 CARD 等参考数据库进行比对，从而识别 AMR 基因匹配。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 实现支持在高性能计算（HPC）和容器化环境中进行可重复、可扩展的多样本批量处理工作流。它利用模块化流水线设计，支持自动化数据库设置、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级监测流水线之间的差距，使其适用于研究和公共卫生基因组学应用。
英文摘要：
Studies that relate bacterial genomes to antimicrobial susceptibility test (AST) results need determinant calls and phenotypes that can be traced to the exact genome, software, database and source export they came from. AMRScan 2 is a rewrite of the AMRScan toolkit for this purpose. Its Nextflow workflow runs NCBI AMRFinderPlus on genome assemblies in a pinned container, writes a provenance record for every sample with the command, the software version and the SHA-256 hashes of the input, of every database file and of the report, and converts each report into a table with a fixed schema that keeps every original column. The conversion step stops if a report no longer matches its provenance record. A second tool archives AST and isolate tables exported from NCBI Pathogen Detection, checks each export against an independent count, and builds isolate and endpoint tables offline that can be rebuilt and compared byte for byte. AMRScan does not infer phenotype from determinants; calls and phenotypes are kept as separate layers and joined by assembly accession. The caller wrapper was used to call 10,521 public Escherichia coli assemblies on a workstation without a failed call, and a run of 1,000 of these assemblies through the workflow on an HPC system gave byte-identical reports. The workflow follows nf-core conventions and is tested with unit tests, nf-test and continuous integration. This version replaces the 2025 description of AMRScan 1, a BLAST search against CARD, which is kept unchanged in the repository.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
