PloidyPatch: duplication-aware plant gene-model repair tool
PloidyPatch tackles the problem of lost or collapsed gene models in duplicated plant genomes by creating auditable, reversible GFF3 patches. It integrates predictions from multiple annotation tools, keeps distinct CDS chains, and records reviewer decisions for reproducibility. The workflow is command‑line driven, works with standard bioinformatics formats, and is aimed at plant genomics researchers needing reliable annotation repair. Its patch‑based approach ensures no permanent changes to source files, setting it apart from typical annotation pipelines.
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