Reference Genomes

LAPIS and SILO need a reference_genomes.json file. It contains the reference sequences of the underlying organism. This page contains the technical specification of the reference genomes file.

The reference genomes are considered static configuration that don’t change with data updates.

This is a minimal valid example:

{
    "nucleotideSequences": [
        {
            "name": "segment1",
            "sequence": "ATCG"
        }
    ],
    "genes": [
        {
            "name": "gene1",
            "sequence": "MYSF*"
        }
    ]
}

The file must contain a JSON object with two keys:

Key	Type	Required	Description
nucleotideSequences	array	true	An array of reference sequences
genes	array	true	An array of reference sequences

Reference Sequence

A reference sequence is a JSON object that permits the following keys:

Key	Type	Required	Description
name	string	true	The name of the sequence. Must be unique.
sequence	string	true	The sequence. See here for allowed characters.