ERMA: a harmonizing epicPCR data analysis tool
We present ERMA, an open-source, Snakemake-based pipeline that enables an automated, standardized, reproducible and scalable epicPCR data analysis with minimal user input. ERMA supports both Illumina and ONT sequencing data and integrates quality control, database preparation, dual similarity searches against taxonomic and functional reference databases, results integration, filtering and visualization. The pipeline is adaptable to a broad range of research questions beyond AMR due to modular database preparation and integration of specific UniRef queries. We evaluated ERMA using five publicly available epicPCR datasets covering diverse sample sources and sequencing depths. Across these datasets, ERMA achieved mean concordance rates of approximately 70–83% with the taxonomic results reported in the respective publications. In selected cases concordance exceeded 86%. In addition, validation using a defined five-member mock community spiked into clinical wastewater demonstrated full recovery of mock genera and a mean genus-level overlap of 85% between ERMA and independent 16S rDNA gene analysis of the same WW sample alone. Attrition analysis showed inconsistent filtering patterns across studies, reflecting dataset-specific quality differences.