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

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ID: 334130
2026
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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: From https://github.com/jltsiren/gbz-base and https://crates.io/crates/gbz-base under the MIT license.
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Authors Jouni Sirén, Benedict Paten, Derek Albracht, Ivan A Alexandrov, Jamie Allen, Alawi A Alsheikh-Ali, Nicolas Altemose, Casey Andrews, Dmitry Antipov, Lucinda Antonacci-Fulton, Mobin Asri, Marcelo Ayllon, Jennifer R Balacco, Floris P Barthel, Edward A Belter, Halle D Bender, Andrew P Blair, Davide Bolognini, Katherine E Bonini, Christina Boucher, Guillaume Bourque, Silvia Buonaiuto, Shuo Cao, Andrew Carroll, Ann M Mc Cartney, Monika Cechova, Mark J P Chaisson, Pi-Chuan Chang, Xian Chang, Jitender Cheema, Haoyu Cheng, Claudio Ciofi, Hiram Clawson, Sarah Cody, Vincenza Colonna, Holland C Conwell, Robert Cook-Deegan, Mark Diekhans, Maria Angela Diroma, Daniel Doerr, Zheng Dong, Danilo Dubocanin, Richard Durbin, Jana Ebler, Evan E Eichler, Jordan M Eizenga, Parsa Eskandar, Eddie Ferro, Anna-Sophie Fiston-Lavier, Sarah M Ford, Willard W Ford, Giulio Formenti, Adam Frankish, Mallory A Freeberg, Qichen Fu, Stephanie M Fullerton, Robert S Fulton, Shenghan Gao, Yan Gao, Gage H Garcia, Obed A Garcia, Joshua M V Gardner, Shilpa Garg, Erik Garrison, Nanibaa’ A Garrison, John E Garza, Margarita Geleta, Mohammadmersad Ghorbani, Tina A Graves-Lindsay, Richard E Green, Carol W Greider, Cristian Groza, Bida Gu, Andrea Guarracino, Melissa Gymrek, Maximilian Haeussler, Leanne Haggerty, Ira M Hall, Nancy F Hansen, Yue Hao, Mohammad Amiruddin Hashmi, David Haussler, Prajna Hebbar, Peter Heringer, Glenn Hickey, Todd L Hillaker, S Nakib Hossain, Neng Huang, Sarah E Hunt, Toby Hunt, Alexander G Ioannidis, Nafiseh Jafarzadeh, Nivesh Jain, Erich D Jarvis, Maryam Jehangir, Juan Jiang, Eimear E Kenny, Juhyun Kim, Bonhwang Koo, Sergey Koren
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag796
URL
https://doi.org/10.1093/bioinformatics/btag796
Keywords Keywords not found

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