From de Bruijn graphs to variation graphs-relationships between pangenome models
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866916656551297024 |
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| author | Cicherski, Adam Dojer, Norbert |
| author_facet | Cicherski, Adam Dojer, Norbert |
| contents | Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two graph-based models are particularly widely used: variation graphs and de Bruijn graphs. In the current paper we propose an axiomatization of the desirable properties of a graph representation of a collection of strings. We show the relationship between variation graphs satisfying these criteria and de Bruijn graphs. This relationship can be used to efficiently build a variation graph representing a given set of genomes, transfer annotations between both models, compare the results of analyzes based on each model etc. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_14520 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | From de Bruijn graphs to variation graphs-relationships between pangenome models Cicherski, Adam Dojer, Norbert Genomics Combinatorics Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two graph-based models are particularly widely used: variation graphs and de Bruijn graphs. In the current paper we propose an axiomatization of the desirable properties of a graph representation of a collection of strings. We show the relationship between variation graphs satisfying these criteria and de Bruijn graphs. This relationship can be used to efficiently build a variation graph representing a given set of genomes, transfer annotations between both models, compare the results of analyzes based on each model etc. |
| title | From de Bruijn graphs to variation graphs-relationships between pangenome models |
| topic | Genomics Combinatorics |
| url | https://arxiv.org/abs/2503.14520 |