RecGraph: recombination-aware alignment of sequences to variation graphs

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 cap...

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Bibliographic Details
Published in:	Bioinformatics (Oxford, England) Vol. 40; no. 5
Main Authors:	Avila Cartes, Jorge, Bonizzoni, Paola, Ciccolella, Simone, Della Vedova, Gianluca, Denti, Luca, Didelot, Xavier, Monti, Davide Cesare, Pirola, Yuri
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 02-05-2024 Oxford Publishing Limited (England)
Subjects:	Algorithms Alignment Availability Bacteria Dynamic programming Gene sequencing Genome, Bacterial Genomes Genomics - methods Graphical representations Humans Introduced species Original Paper Recombination Recombination, Genetic Sequence Alignment - methods Sequence Analysis, DNA - methods Software Variability Variation
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1367-4811 1367-4803 1367-4811
DOI:	10.1093/bioinformatics/btae292