Welcome to SchemaRefinery’s documentation!

Overview:

• Overview
• Installation Guide
• Contact and Support

Modules:

• DownloadAssemblies - Download assemblies and their metadata from specified databases
• AdaptLoci - Adapt fastas into a chewBBACA schema
• MatchSchemas - Match schemas in a directory
• IdentifyParalogousLoci - Identify paralogous loci in a schema
• IdentifySpuriousGenes - Identify spurious genes in a schema
• SchemaAnnotation - Annotate schemas
• ApplyRecommendations - Create a new schema based on recommendations

Tutorials:

• Schema Refinery - Full Tutorial
• DownloadAssemblies - Tutorial
• AdaptLoci - Tutorial
• MatchSchemas - Tutorial
• IdentifyParalogousLoci - Tutorial
• IdentifySpuriousGeneSchema - Tutorial
• IdentifySpuriousGenesUnclassifiedCDS - Tutorial
• SchemaAnnotation - Tutorial
• ApplyRecommendations - Tutorial

External Links:

ChewBBACA Related Links:

• chewBBACA documentation

• chewBBACA GitHub repository

• ChewieNS documentation

• ChewieNS website

SchemaRefinery Related Links:

• NCBI datasets

• Python

• Biopython

• Requests

• SchemaRefinery GitHub repository