File Formats¶

Supported File Types¶

Core Genome Files¶

Extension	Description	Required
`.fna`	Assembly FASTA	Yes
`.gbk`	GenBank file	Yes
`.gff`	General Feature Format	Yes
`.faa`	Protein sequences FASTA	No*
`.ffn`	Nucleotide sequences FASTA	No*
`.sqn`	GenBank submission file	No

*Generated automatically from .gbk if not present

Annotation Files¶

Extension	Description	Source
`.emapper.annotations`	Eggnog annotations	Eggnog
`.XX`	Custom annotations	Various
`_busco.txt`	BUSCO results	BUSCO

Metadata Files¶

Filename	Description	Purpose
`genome.json`	Genome metadata	Custom genome information
`organism.json`	Organism metadata	Custom organism information

File Naming Conventions¶

Locus Tags¶

Should start with the genome identifier
Example: STRAIN.1_00001
Used consistently across all file types

Custom Annotations¶

Files with two uppercase letter extensions (e.g., .EC, .GO)
Automatically detected during import
Renamed to match genome locus tags

File Organization¶

Default Structure¶

organisms/
└── STRAIN/
    ├── organism.json
    └── genomes/
        └── STRAIN.1/
            ├── genome.json
            ├── STRAIN.1.fna
            ├── STRAIN.1.gbk
            ├── STRAIN.1.gff
            ├── STRAIN.1.faa
            ├── STRAIN.1.ffn
            └── rest/

Custom Organization¶

See Quick Start for information on custom file organization.