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

TL;DR

AMRScan is a versatile toolkit combining R and Nextflow for rapid, scalable detection of antimicrobial resistance genes from sequencing data, suitable for research and public health use.

Contribution

It introduces a hybrid R and Nextflow toolkit that enables both quick single-sample analysis and scalable multi-sample workflows for AMR gene detection.

Findings

Supports rapid identification of AMR genes in sequencing data

Provides reproducible workflows for high-throughput analysis

Bridges exploratory analysis and surveillance pipelines

Abstract

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.