FRED enables standardized FAIR metadata generation and management for omics research.

Scientific research relies on transparent dissemination of data and its associated interpretations, including raw data, metadata, experimental design, and data processing details. Production and handling of research data represents an ongoing challenge, extending beyond publication into individual facilities, institutes and research groups, often termed Research Data Management (RDM). It is foundational to scientific discovery and aligned with the FAIR principles. Although the majority of peer-reviewed journals require raw data deposition in public repositories in alignment with FAIR principles, metadata frequently lacks standardization, hindering effective utilization and sharing of research findings. Here we present FRED, a generalized toolkit for FAIR metadata management in omics research based on a flexible, machine-readable YAML format. FRED enables (i) guided, dialog-based creation of metadata files, (ii) structured semantic validation, (iii) logical cross-file search, (iv) API-based integration with external systems, and (v) self-hosted web deployment. We demonstrate the utility of FRED through a complete annotation workflow applied to a published single-nucleus RNA-seq dataset, covering metadata generation, validation, repository-based discovery, and export to NCBI GEO submission format. FRED is designed for non-computational scientists and specialized facilities alike, and integrates into existing RDM infrastructure without requiring dedicated IT resources.