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Published on: May 22, 2018
GBZ-base and GAF-base: Indexed pangenome file formats
Jouni Sirén1, Benedict Paten1,
1Genomics Institute, UC Santa Cruz, 1156 High Street, Santa Cruz, 95064, California, USA.
Biorxiv : the Preprint Server for Biology
|July 17, 2026
Summary
New GBZ-base and GAF-base file formats enable direct disk access for pangenome graphs and alignments. This facilitates interactive applications by avoiding memory loading and sequential reading of large datasets.
Area of Science:
- Bioinformatics
- Computational Biology
Background:
- Existing pangenome file formats require loading entire graphs into memory and sequential reading of alignment files, hindering interactive applications.
- Current formats are optimized for batch processing, lacking efficiency for real-time data manipulation.
Purpose of the Study:
- To introduce novel, disk-based file formats for pangenome graphs and sequence alignments.
- To enable efficient, direct-access operations on large pangenome datasets for interactive use cases.
Main Methods:
- Development of SQLite-backed file formats: GBZ-base for pangenome graphs and GAF-base for sequence alignments.
- Implementation of efficient extraction of local subgraphs from GBZ-base.
- Enabling extraction of all sequence-to-graph alignments to a specific subgraph using GAF-base.
Main Results:
- GBZ-base and GAF-base formats allow direct data access from disk, bypassing memory limitations.
- GBZ-base facilitates efficient retrieval of localized pangenome subgraph data.
- GAF-base provides efficient extraction of sequence alignments to subgraphs and is the most compact format for sequence-to-graph alignments.
Conclusions:
- GBZ-base and GAF-base offer a significant improvement for interactive pangenome analysis.
- These new formats address the limitations of existing batch-oriented pangenome file structures.
- The proposed formats enhance usability and efficiency in computational biology workflows.
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