DOI: 10.1093/bioinformatics/btag796 ISSN: 1367-4811
GBZ-base and GAF-base: Indexed pangenome file formats
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, Milinn Kremitzki, Charles H Langley, Ben Langmead, Heather A Lawson, Daofeng Li, Heng Li, Wen-Wei Liao, Jiadong Lin, Tianjie Liu, Glennis A Logsdon, Ryan Lorig-Roach, Jonathan LoTempio, Hailey Loucks, Jane E Loveland, Jianguo Lu, Shuangjia Lu, Julian K Lucas, Walfred Ma, Juan F Macias-Velasco, Kateryna D Makova, Maximillian G Marin, Christopher Markovic, Tobias Marschall, Franco L Marsico, Fergal J Martin, Mira Mastoras, Capucine Mayoud, Brandy McNulty, Jack A Medico, Julian M Menendez, Karen H Miga, Anna Minkina, Matthew W Mitchell, Saswat K Mohanty, Younes Mokrab, Jean Monlong, Shabir Moosa, Avelina Moreno-Ochando, Shinichi Morishita, Jonathan M Mudge, Katherine M Munson, Njagi Mwaniki, Nasna Nassir, Chiara Natali, Shloka Negi, Lingbin Ni, Adam M Novak, Faith Okamoto, Keisuke K Oshima, Pilar N Ossorio, Chie Owa, Sadye Paez, Benedict Paten, Clelia Peano, Adam M Phillippy, Brandon D Pickett, Laura Pignata, Nadia Pisanti, David Porubsky, Pjotr Prins, Timofey Prodanov, Anandi Radhakrishnan, T Rhyker Ranallo-Benavidez, Brian J Raney, Mikko Rautiainen, Alessandro Raveane, Andreas Rechtsteiner, Luyao Ren, Arang Rhie, Fedor Ryabov, Samuel Sacco, Farnaz Salehi, Michael C Schatz, Laura B Scheinfeldt, Aarushi Sehgal, William E Seligmann, Mahsa Shabani, Kishwar Shafin, Shadi Shahatit, Ruhollah Shemirani, Vikram S Shivakumar, Swati Sinha, Jouni Sirén, Linnéa Smeds, Steven J Solar, Marco Sollitto, Nicole Soranzo, Andrew B Stergachis, Marie-Marthe Suner, Yoshihiko Suzuki, Arda Söylev, Ahmad Abou Tayoun, Jack A S Tierney, Chad Tomlinson, Francesca Floriana Tricomi, Mohammed Uddin, Matteo Tommaso Ungaro, Rahul Varki, Flavia Villani, Ivo Violich, Mitchell R Vollger, Brian P Walenz, Charles Wang, Lisa E Wang, Ting Wang, Aaron M Wenger, Conor V Whelan, Zilan Xin, Zheng Xu, Kai Ye, DongAhn Yoo, Wenjin Zhang, Ying Zhou, Xiaoyu Zhuo, Giulia ZuninoAbstract
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.