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PreprintCC BYbioRxiv

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

  • J. Siren
  • B. Paten
  • the Human Pangenome Reference Consortium
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Abstract

Motivation: Existing 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. Results: We 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 implementation: https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.

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Cite

BibTeXRIS
BibTeX
@misc{siren2026gbzbase,
  title = {{GBZ-base and GAF-base: Indexed pangenome file formats}},
  author = {J. Siren and B. Paten and the Human Pangenome Reference Consortium},
  howpublished = {bioRxiv},
  year = {2026},
  month = jul,
  doi = {10.64898/2026.07.10.737775},
  url = {https://www.biorxiv.org/content/10.64898/2026.07.10.737775v2},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - GBZ-base and GAF-base: Indexed pangenome file formats
AU  - J. Siren
AU  - B. Paten
AU  - the Human Pangenome Reference Consortium
PY  - 2026
DA  - 2026/07/10
PB  - bioRxiv
DO  - 10.64898/2026.07.10.737775
UR  - https://www.biorxiv.org/content/10.64898/2026.07.10.737775v2
AB  - Motivation: Existing 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. Results: We 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 implementation: https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.
ER  -