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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:

nucleotideSequencesarraytrueAn array of reference sequences
genesarraytrueAn array of reference sequences

Reference Sequence

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

namestringtrueThe name of the sequence. Must be unique.
sequencestringtrueThe sequence. See here for allowed characters.