albertolupatin/metaref-db

MetaRefSGB Jan26 — queryable SQLite build

metaref_full.db is the MetaRefSGB Jan26 release packed into a single SQLite file with indexes and FTS5 search — ready to query directly, no extraction or import step.

Download it and open it read-only, or range-request it over HTTPS (this repo serves Accept-Ranges: bytes with open CORS, so it can be read a page at a time without downloading all 1.7 GB).

Table	Rows
sgbs	265,780
genomes	2,170,082
samples	536,841
datasets	60,386
markers	13,310,440
sample_sgbs / dataset_sgbs	1,313,070 / 380,921

Schema notes

• genomes.release is the release a genome was added in — the table is cumulative across releases. Genomes new in Jan26: 561,185. Total MAGs of any release: 1,950,098. sgbs.n_jan26 follows the former definition.
• markers is WITHOUT ROWID, keyed (sgb, uniref) — lookups by SGB are an index seek and the table carries no duplicate primary-key index.
• FTS5 indexes (sgbs_fts, genomes_fts, samples_fts, datasets_fts) are contentless; join back on rowid.

Use

from huggingface_hub import hf_hub_download
import sqlite3

path = hf_hub_download("albertolupatin/metaref-db", "metaref_full.db", repo_type="dataset")
con = sqlite3.connect(f"file:{path}?mode=ro", uri=True)
con.execute("SELECT COUNT(*) FROM genomes WHERE release='Jan26'").fetchone()

Source

Built from the MetaRefSGB Jan26 release files (sequences.txt, SGB.Jan26.txt, metadata.tsv) and the ChocoPhlAn/MetaPhlAn marker databases.

Cite: Dmitrijeva, Ruscheweyh et al. (2025), Nucleic Acids Research, doi:10.1093/nar/gkae1004