GFF3 Merge Tool

The GFF3 merge tool consolidates multiple annotation files into a single, unified GFF3 dataset. It accepts one or more plain text GFF3 files, and optionally gzip-compressed inputs, and outputs a single, standards-compliant GFF3 file ready for downstream analyses. The tool preserves core feature data (seqid, source, type, start, end, score, strand, phase) and all attribute columns, while resolving overlaps and duplicates in a deterministic manner.
Core concept and workflow: the engine parses each feature, groups by key fields, and merges entries according to a defined policy. When features share an ID and type but differ in attributes, non-conflicting attributes are merged; conflicting values can be logged and optionally resolved by user-defined rules. The merged output is sorted by seqid, start, and end, with header lines preserved.
Who benefits and differentiators: scientists performing cross-dataset integration, annotation curation teams, and bioinformatics engineers building reproducible pipelines gain a reliable, auditable merge process. Unique value includes strict GFF3 validation, transparent merge logs, support for filtering (by sequence, type, or source), and an explicit report of changes to aid provenance and audits.
Use cases include integrating annotations from multiple assemblies, consolidating feature catalogs for a genome project, and preparing data for comparative genomics studies. The tool emphasizes data integrity, deterministic results, and compliance with GFF3 standards to reduce post-processing errors.