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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...in the population (Singh et al. 2022). A variety of methods have been developed that use pan graphs for common applications, including genotyping, variant calling, haplotype reconstruction, metagenomic read classification, etc. (Eizenga et al. 2020). Efforts toward using pan graphs have been further catalyzed...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...community, we anticipate VRPG to be further improved, facilitating researchers from different fields to better explore the power of graph-based pangenomics, especially in the age of large-scale long-read-based population sequencing (Rech et al. 2022; O'Donnell et al. 2023; Weller et al. 2023; Gustafson et...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
.... briggsae strains and nine C. nigoni strains, including both reference strains. Through comparative pan-genomic analyses of both nematode species, we aim to identify the critical structural and genetic variations that drive intra- and interspecific evolution, ultimately leading to speciation...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...pangenomics: a tutorial on data structures and their applications. Nat Comput 21: 81–108. doi:10.1007/s11047-022-09882-6 ↵Bradbury PJ, Casstevens T, Jensen SE, Johnson L, Miller Z, Monier B, Romay M, Song B, Buckler ES. 2022. The practical haplotype graph, a platform for storing and using pans for imputation...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...references. Consequently, two pangenomic aligners have been developed within the vg toolkit: vg map (Garrison et al. 2018; Sirén et al. 2020) and vg giraffe (Sirén et al. 2021). Both methods involve constructing and aligning to a variation graph. In this graph, nodes represent segments of DNA sequences...
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Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
- Juri Kuronen,
- Samuel T. Horsfield,
- Anna K. Pöntinen,
- Sudaraka Mallawaarachchi,
- Sergio Arredondo-Alonso,
- Harry Thorpe,
- Rebecca A. Gladstone,
- Rob J.L. Willems,
- Stephen D. Bentley,
- Nicholas J. Croucher,
- Johan Pensar,
- John A. Lees,
- Gerry Tonkin-Hill,
- and Jukka Corander
Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
...colored de Bruijn graph construction algorithm, Cuttlefish, provides an optimal starting point for a pangenomic GWES that does not rely on a single-reference -based representation of variation (Khan and Patro 2021). Using this data structure, we have developed an efficient algorithm, PAN...
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Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
- Daniela S. Aliaga Goltsman,
- Christine L. Sun,
- Diana M. Proctor,
- Daniel B. DiGiulio,
- Anna Robaczewska,
- Brian C. Thomas,
- Gary M. Shaw,
- David K. Stevenson,
- Susan P. Holmes,
- Jillian F. Banfield,
- and David A. Relman
Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
...an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from...
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Method: Efficient taxa identification using a pangenome index
- Omar Ahmed,
- Massimiliano Rossi,
- Christina Boucher,
- and Ben Langmead
Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
...at the strain level with higher accuracy compared with other approaches. Finally, we present strategies for compacting this structure in applications in which read lengths or match lengths can be bounded.Metagenomic read (Wood et al. 2019) classification allows researchers to study organisms present...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...and Salzberg 2020). These pans are frequently modeled as graphs (Garrison et al. 2018; Li et al. 2020), which work well to represent and detect structural variants (SVs), sequence alterations >50 bp, compared with reference-based short-read alignment (Mérot et al. 2020). Pangenomic approaches have proven...
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