rMAP (Rapid Microbial Analysis Pipeline) is a modular, reproducible bioinformatics workflow suite for microbial whole-genome sequencing analysis, supporting routine genomic epidemiology and public-health workflows. rMAP streamlines common steps including read QC, trimming, de novo assembly, species/lineage typing (e.g., MLST), resistance gene detection, plasmid replicon screening, virulence profiling, and reporting.
rMAP is available in three deployable implementations to support different users and computing environments:
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rMAP-1.0 (Bash-based CLI) — a lightweight command-line implementation for rapid local analyses and quick turnaround in low-resource settings. Designed to run on a standard Linux workstation or server, it supports straightforward execution with minimal dependencies and is well-suited for routine QC, assembly, and downstream screening steps in small-to-medium WGS datasets.
https://github.com/GunzIvan28/rMAP -
rMAP Web — a browser-accessible interface for guided analysis with no local setup required. The rMAP Genome Analysis Platform supports uploading
.fastqfiles and running end-to-end microbial genomics workflows for researchers, organizations, and data scientists. Users can upload data, launch analyses on large datasets, and receive notifications when jobs complete.
https://genomeclarity.com/ -
rMAP-2.0 (Docker + Cromwell/WDL) — containerized, workflow-orchestrated implementation designed for reproducible and scalable execution. Its implementation emphasizes portability and reproducibility by running version-controlled workflows in containerized environments, enabling consistent results across laptops, servers, and cloud platforms. The pipeline produces standardized QC summaries and analysis outputs suitable for surveillance reporting, research projects, and training.
https://github.com/gmboowa/rMAP-2.0
rMAP-1.0 Publication: Here