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MMASeq (Mixed Microbial Analysis on Sequencing data) is a fully modular and reproducible bioinformatics pipeline for bacterial isolate characterization developed at Statens Serum Institute as part of the MicrobeSeq Denmark project The pipeline is designed for flexibility and transparency, and it leverages Snakemake for workflow management. Indeed, it integrates various tools for antimicrobial resistance profiling, sequence typing, virulence detection, and more.

The main objective is to provide a reproducible, modular framework for bacterial Whole Genome Sequencing (WGS) analysis within national surveillance. Its species-specific design and automated dependency management ensure transparent, scalable, and standardized workflows that can be easily adapted to emerging pathogens and implemented in other laboratory settings.