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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.
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:
From https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.
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