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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
...and querying of compacted and colored de Bruijn graphs with GGCAT. Genome Res 33: 1198–1207. doi:10.1101/gr.277615.122 ↵Croucher NJ, Walker D, Romero P, Lennard N, Paterson GK, Bason NC, Mitchell AM, Quail MA, Andrew PW, Parkhill J, et al. 2009. Role of conjugative elements in the evolution of the multidrug...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...to the particular advantages of variation graphs in the analysis of metas. The implementation of PanTax is fundamentally enabled by the topology of variation graphs. As a specific form of graph, variation graphs collapse homologous regions and represent them as alternative paths within the graph. When constructed...
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RECOMB 2022 Special/Methods: Lossless indexing with counting de Bruijn graphs
- Mikhail Karasikov,
- Harun Mustafa,
- Gunnar Rätsch,
- and André Kahles
Genome Res. September 2022 32: 1754-1764; Published in Advance May 24, 2022, doi:10.1101/gr.276607.122
...). Counting de Bruijn graphs index k-mer abundances from 2652 human RNA-seq samples in over eightfold smaller representations compared with state-of-the-art bioinformatics tools and is faster to construct and query. Furthermore, counting de Bruijn graphs with positional annotations losslessly represent entire...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
....MethodsThe original Verkko pipeline consisted of six main steps, with module dependencies given in parentheses: homopolymer compression and correction of LA reads (HiCanu) (Nurk et al. 2020), LA multiplex De Bruijn graph construction (MBG) (Rautiainen and Marschall 2021), alignment of UL reads to the LA graph (Graph...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...all pairs of individuals across the can be utilized to construct graphs of genetic similarity, in which individuals are represented as nodes, and shared IBD haplotypes are represented as edges (Belbin et al. 2021). Previous studies have shown the advantages of utilizing IBD data to represent recent...
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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
...component gadgets, we define our vector gadgets: The query sequence is defined as . For 1 ≤ i ≤ n, we construct haplotype sequence Hi from vector ai: To create the vertices of graph G, we start with the following: a vertex denoted vleft with label 0nd; 2d vertices denoted vx,0, vx,1 for 1 ≤ x ≤ d, where...
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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
...at the per-base level. As an improvement, Minigraph-Cactus was proposed as an extended solution that combines the compactness and efficiency of Minigraph as well as the base-level sensitivity and accuracy of Cactus. Pan graphs constructed by Minigraph-Cactus can effectively represent both small and large...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
...of finding accurate alignments. Methods that use de Bruijn graphs (DBGs) as a graph model (Bowe et al. 2012) or use an auxiliary index (Sirén 2017) are restricted to finding seeds of minimum length k. To find seeds when the query has a high edit distance relative to the reference sequences, sequence-to-graph...
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Review: Data structures based on k-mers for querying large collections of sequencing data sets
- Camille Marchet,
- Christina Boucher,
- Simon J. Puglisi,
- Paul Medvedev,
- Mikaël Salson,
- and Rayan Chikhi
Genome Res. January 2021 31: 1-12; Published in Advance December 16, 2020, doi:10.1101/gr.260604.119
...these signatures. They confirmed some fusions and reported some novel ones. Fusion transcripts provide interesting targets for cancer immunotherapies because they are prone to exhibit tumor-specific markers.One of the data structures covered in this survey, the colored de Bruijn graph, has also been used for rapid...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
..., RDG-Viewer (available at https://colab.research.google.com/drive/1f5iSgy5DAXeq27Lx1fCyngm4IjinkgC5?usp=sharing). This Google Collaboratory notebook uses graph construction functionality from the RDG Python package (https://pypi.org/project/RDG/), which is currently under development (https...
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