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bioRxiv · 10.64898/2026.07.10.737775

GBZ-base and GAF-base: Indexed pangenome file formats

Siren, J.·Paten, B.·the Human Pangenome Reference Consortium,
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Abstract

MotivationExisting pangenome file formats are designed for batch processing. Graphs must be loaded into memory, and alignment files must be read sequentially. Indexed file formats that can be used directly from disk would be more appropriate for interactive applications. ResultsWe propose GBZ-base and GAF-base -- SQLite-backed file formats comparable to GBZ and GAF. GBZ-base supports efficient extraction of local subgraphs, and GAF-base lets us extract all alignments to the subgraph. Additionally, GAF-base is smaller than any other file format for sequence-to-graph alignments. Availability and implementationFrom https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.

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Siren, J., Paten, B., the Human Pangenome Reference Consortium,. 2026-07-11. GBZ-base and GAF-base: Indexed pangenome file formats. https://doi.org/10.64898/2026.07.10.737775

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