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

GBZ-base and GAF-base are SQLite-backed pangenome file formats that enable efficient on-disk extraction of local subgraphs and their alignments.

• Why it matters: Existing pangenome formats are built for batch processing, requiring graphs to be loaded into memory and alignments to be read sequentially, limiting interactive use.
• What they did: The work proposes GBZ-base for efficient local subgraph extraction and GAF-base for extracting all alignments to a subgraph, with GAF-base reported as smaller than any other sequence-to-graph alignment format.
• The result: These indexed formats can be used directly from disk, supporting interactive applications by avoiding full in-memory graph loading and enabling targeted alignment retrieval.