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Poster De Conférence Année : 2024

Benchmarking pangenome graph mapping with strobemer-based seeding

Résumé

A pangenome represents the total genetic diversity of a species or a species complex. A recent model, the variation graph, aims to integrate full length genomes. Contrary to typical mapping approaches which rely on a single reference genome and are intrinsically biased, mapping query sequences to the full genetic variability of a species leads to more accurate mappings and improved genotype /phenotype analyses. Mapping to a graph is similar to classic genome mapping and the first step involves a seed & extend approach, to target regions in the graph involving similar sequences before the steps of path selection and alignment. When divergent query sequences are analyzed, this step can be problematic : not enough k-mer seeds are detected, and the following steps do not happen. This work aims to test the potential of strobemers, an alternative to classic k-mer+minimizer seeding that allows more sequence divergence, in the context of mapping to pangenome graphs.
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Dates et versions

hal-04656363 , version 1 (22-07-2024)

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  • HAL Id : hal-04656363 , version 1

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Marouane Boumlik, Benjamin Linard, Matthias Zytnicki. Benchmarking pangenome graph mapping with strobemer-based seeding. JOBIM 2024, Jun 2024, JOBIM 2024, France. ⟨hal-04656363⟩
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