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BioinformaticsBioinformaticsPeer-reviewed journal article

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

Jouni SiréniD, Benedict PateniD, Derek Albracht, Ivan A Alexandrov, Jamie AlleniD, Alawi A Alsheikh-Ali, Nicolas AltemoseiD, Casey Andrews, Dmitry AntipoviD, Lucinda Antonacci-Fulton, Mobin AsriiD, Marcelo AylloniD, Jennifer R Balacco, Floris P BartheliD, Edward A Belter, Halle D Bender, Andrew P Blair, Davide BologniniiD, Katherine E Bonini, Christina BoucheriD, Guillaume BourqueiD, Silvia BuonaiutoiD, Shuo CaoiD, Andrew Carroll, Ann M Mc Cartney, , Sergey KoreniD

PDFDOIPreprintCode

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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