GBZ file format for pangenome graphs
Open accessPublished version of a preprint
Abstract
MOTIVATION: Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently. RESULTS: We propose the GBZ file format based on data structures used in the Giraffe short-read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems. AVAILABILITY AND IMPLEMENTATION: C++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs, respectively. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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vg giraffe maps only to kmers traversed by the graph's embedded walks with a GBWT or GBZ index, reducing false positives.
“A faster alternative, vg giraffe, was developed to map only to kmers traversed by the graph’s embedded walks with the help of a GBWT or GBZ index, thus reducing false positives [20–22].”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [22]
Section 2.1.6 (page unavailable) says Giraffe uses a GBWT-indexed graph induced by its paths, and the Discussion (page unavailable) identifies GBZ as Giraffe’s preferred graph format. The paper does not say that Giraffe maps only to k-mers traversed by embedded walks or that this reduces false positives. (LLM, conf=0.85)
Experimental — accuracy not yet measuredvg map aligns read kmers against all kmers in the reference graph, including those not in constituent haplotypes, leading to exponential growth in novel kmers during indexing and storage/complexity issues.
“The subcommand vg map aligns read kmers against all kmers in the reference graph, including those that do not exist in any constituent haplotypes, which can lead to exponential growth in novel kmers during indexing of the graph and therefore significant storage and complexity issues.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [22]
The Introduction discusses graph-based read alignment, and §3.5 discusses GBWT index size, but neither describes how vg map indexes read k-mers. Searches for “vg map” and “novel k-mers” found no passage addressing non-haplotype k-mers, exponential growth, or the claimed storage consequences. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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Cites
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0201-4 · Cited by 15,022 · see citing works
A Block-sorting Lossless Data Compression Algorithm
Burrows, M. T., & Wheeler, D. J. (1994) · Cited by 2,333 · see citing works
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
Variation graph toolkit improves read mapping by representing genetic variation in the reference
Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4227 · Cited by 821 · see citing works
Ferragina, P., & Manzini, G. (2005) · Journal of the ACM · doi:10.1145/1082036.1082039 · Cited by 709 · see citing works
The Human Pangenome Project: a global resource to map genomic diversity
Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature · doi:10.1038/s41586-022-04601-8 · Cited by 494 · see citing works
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science · doi:10.1126/science.abg8871 · Cited by 400 · see citing works
Self-citationPangenome Graph Construction from Genome Alignment with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Marschall, T., Li, H., & Paten, B. (2022) · doi:10.1101/2022.10.06.511217 · Cited by 345 · see citing works
Self-citationPangenome graph construction from genome alignments with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01793-w · Cited by 343 · see citing works
Eizenga, J. M., Novak, A. M., Sibbesen, J. A., Heumos, S., Ghaffaari, A., Hickey, G., Chang, X., Seaman, J. D., Rounthwaite, R., Ebler, J., et al. (2020) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120219-080406 · Cited by 320 · see citing works
Self-citationGenotyping structural variants in pangenome graphs using the vg toolkit
Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020) · Genome Biology · doi:10.1186/s13059-020-1941-7 · Cited by 319 · see citing works
Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277 · see citing works
Graphtyper enables population-scale genotyping using pangenome graphs
Eggertsson, H. P., Jónsson, H., Kristmundsdóttir, S., Hjartarson, E., Kehr, B., Másson, G., Zink, F., Hjörleifsson, K. E., Jónasdóttir, Á., Jónasdóttir, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3964 · Cited by 276 · see citing works
Practical Entropy-Compressed Rank/Select Dictionary
Okanohara, D., & Sadakane, K. (2007) · Society for Industrial and Applied Mathematics eBooks · doi:10.1137/1.9781611972870.6 · Cited by 269 · see citing works
GraphAligner: rapid and versatile sequence-to-graph alignment
Rautiainen, M., & Marschall, T. (2020) · Genome Biology · doi:10.1186/s13059-020-02157-2 · Cited by 242 · see citing works
Paragraph: a graph-based structural variant genotyper for short-read sequence data
Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196 · see citing works
Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space
Gagie, T., Navarro, G., & Prezza, N. (2020) · Journal of the ACM · doi:10.1145/3375890 · Cited by 143 · see citing works
High Throughput Short Read Alignment via Bi-directional BWT
Lam, T., Li, R., Tam, A., Wong, S., Wu, E., & Yiu, S. (2009) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2009.42 · Cited by 111 · see citing works
Optimized succinct data structures for massive data
Gog, S., & Petri, M. (2013) · Software Practice and Experience · doi:10.1002/spe.2198 · Cited by 106 · see citing works
Sirén, J., Garrison, E., Novak, A. M., Paten, B., & Durbin, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz575 · Cited by 92 · see citing works
A Draft Human Pangenome ReferencePreprint
Liao, W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J., Monlong, J., Abel, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.09.499321 · Cited by 58 · see citing works
Efficient dynamic variation graphs
Eizenga, J. M., Novak, A. M., Kobayashi, E., Villani, F., Cisar, C., Heumos, S., Hickey, G., Colonna, V., Paten, B., & Garrison, E. P. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa640 · Cited by 30 · see citing works
A Framework of Dynamic Data Structures for String ProcessingPreprint
Prezza, N. (2017) · arXiv (Cornell University) · doi:10.4230/lipics.sea.2017.11 · Cited by 5 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Gog,S. et al. (2014) From theory to practice: plug and play with succinct data structures. In: Proceedings of SEA 2014, vol. 8504 of LNCS. Springer, Cham, pp. 326-337.
Cited by
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A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
A Draft Human Pangenome ReferencePreprint
Liao, W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J., Monlong, J., Abel, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.09.499321 · Cited by 58 · see citing works
Comparing methods for constructing and representing human pangenome graphs
Andreace, F., Lechat, P., Dufresne, Y., & Chikhi, R. (2023) · Genome biology · doi:10.1186/s13059-023-03098-2 · Cited by 59 · see citing works
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
Taylor, D. J., Eizenga, J. M., Li, Q., Das, A., Jenike, K. M., Kenny, E. E., Miga, K. H., Monlong, J., McCoy, R. C., Paten, B., et al. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-021623-081639 · Cited by 50 · see citing works
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01758-0 · Cited by 51 · see citing works
Personalized pangenome references
Sirén, J., Eskandar, P., Ungaro, M. T., Hickey, G., Eizenga, J. M., Novak, A. M., Chang, X. H., Chang, P.-C., Kolmogorov, M., Carroll, A. W., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02407-2 · Cited by 40 · see citing works
Developing pangenomes for large and complex plant genomes and their representation formats
Ruperao, P., Rangan, P., Shah, T. M., Sharma, V., Rathore, A., Mayes, S., & Pandey, M. K. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.01.052 · Cited by 11 · see citing works
Compressive pangenomics using mutation-annotated networks
Walia, S., Motwani, H., Tseng, Y.-H., Smith, K., Corbett-Detig, R. B., & Turakhia, Y. (2026) · Nature Genetics · doi:10.1038/s41588-025-02478-7 · Cited by 10 · see citing works
Pangenome-aware DeepVariantPreprint
Asri, M., Chang, P.-C., Mier, J. C., Sirén, J., Eskandar, P., Kolesnikov, A., Cook, D. E., Brambrink, L., Hickey, G., Novak, A. M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.05.657102 · Cited by 10 · see citing works
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg GiraffePreprint
Chang, X. H., Novak, A. M., Eizenga, J. M., Sirén, J., Monlong, J., Negi, S., Andreace, F., Nag, S., Kyriakidis, K., Hickey, G., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.29.678807 · Cited by 10 · see citing works
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Andreace, F., Lechat, P., Dufresne, Y., & Chikhi, R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.02.542089 · Cited by 4 · see citing works
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3086064/v1 · Cited by 4 · see citing works
Dong, Z., Whitehead, J., Fu, M., MacIsaac, J. L., Rehkopf, D. H., Rosero‐Bixby, L., Kobor, M. S., & Korthauer, K. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.07.617116 · Cited by 4 · see citing works
Dong, Z., Whitehead, J., Fu, M., MacIsaac, J. L., Rehkopf, D. H., Rosero‐Bixby, L., Kobor, M. S., & Korthauer, K. D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115755 · Cited by 3 · see citing works
Genomic insights into the divergence between hulled and hulless oats
Li, W., Liu, J., Liu, N., Liang, H., Zhang, L., Sun, Q., Wei, Y., Li, M., Liu, X., Yun, Y., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116055 · Cited by 3 · see citing works
Moosman, O. W., Kelley, J. L., & Bogan, S. N. (2025) · Heredity · doi:10.1038/s41437-025-00803-8 · Cited by 1 · see citing works
Building and applying pangenome references to capture genetic diversity
Ashraf, H., Doerr, D., Ebler, J., & Marschall, T. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00987-7 · Cited by 1 · see citing works
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Heringer, P., & Doerr, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.22.655470 · Cited by 1 · see citing works
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Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26643784
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26643793
Rice, E. S., Alberdi, A., Alfieri, J. M., Athrey, G., Balacco, J., Bardou, P., Blackmon, H., Charles, M., Cheng, H. H., Fedrigo, O. D., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26643787
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Dimonaco, N. J., Clare, A. J., & Vickers, M. J. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag357
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Harviainen, J., Sena, F., Moumard, C., Politov, A., Schmidt, S., & Tomescu, A. I. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag235
Rigano, G., Giuffrè, L., Strangio, S., Criseo, G., Cascio, G. L., Alati, C., Meliadò, A., Martino, M., Principe, L., & Romeo, O. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1872401
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Bocs, S., Carrette, C., Confais, J., Dubois, S., Duvaux, L., Klopp, C., Lapalu, N., Lasserre‐Zuber, P., Legeai, F., Lemaitre, C., et al. (2026) · Peer Community Journal · doi:10.24072/pcjournal.781
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- Authors
- Sirén, J., & Paten, B.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Sirén, Jouni
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-09-30
- Volume
- 38
- Issue
- 22
- Pages
- 5012-5018
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC9665857
- OpenAlex
- W4298109415
- Cited by
- 35
- References
- 24
- Citations by year
- 2026: 12 · 2025: 10 · 2024: 6 · 2023: 6 · 2022: 1
- FWCI
- 2.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Bioinformatics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute
- National Institutes of Health (U01HG010961, R01HG010485, U41HG010972, U24HG011853, OT2OD026682)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- pangenome graphs, graph compression, giraffe, short-read alignment, genome assembly, in-memory data structures, data storage efficiency
- MeSH terms
- Libraries, Software, Data Compression, High-Throughput Nucleotide Sequencing
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