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Welcome to the RagTag docs!

RagTag, the successor to RaGOO, is a command line tool for reference-guided genome assembly improvement. Currently, the two main features are misassembly correction and scaffolding. After correction and/or scaffolding, RagTag also provides utilities to update annotations or work with AGP files. RagTag is being actively developed to add new features and improve existing features.

Please use the sidebar to find detailed documentation on specific topics.