Motivation Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.Results In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modelling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.Availability and implementation Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.

Avila Cartes, J., Bonizzoni, P., Ciccolella, S., Della Vedova, G., Denti, L., Didelot, X., et al. (2024). RecGraph: recombination-aware alignment of sequences to variation graphs. BIOINFORMATICS, 40(5) [10.1093/bioinformatics/btae292].

RecGraph: recombination-aware alignment of sequences to variation graphs

Avila Cartes J.;Bonizzoni P.;Ciccolella S.;Della Vedova G.
;
Denti L.;Monti D. C.;Pirola Y.
2024

Abstract

Motivation Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.Results In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modelling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.Availability and implementation Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.
Articolo in rivista - Articolo scientifico
bioinformatics; algorithms; pangenomics
English
27-apr-2024
2024
40
5
btae292
none
Avila Cartes, J., Bonizzoni, P., Ciccolella, S., Della Vedova, G., Denti, L., Didelot, X., et al. (2024). RecGraph: recombination-aware alignment of sequences to variation graphs. BIOINFORMATICS, 40(5) [10.1093/bioinformatics/btae292].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/484519
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