RecGraph: adding recombinations to sequence-to-graph alignments

The transition towards graph pangenomes is posing several new challenging questions, most notably how to extend the classical notion of read alignment from a sequence-to-sequence to a sequence-to-graph setting. Especially on variation graphs, where paths corresponding to individual genomes are labeled, notions of alignments that are strongly inspired by the classical ones are usually able to capture only variations that can be expressed by mismatches or gaps, such as SNPs or short insertions and deletions. On the other hand the recent investigation of pangenomes at bacterial scale (Colquhoun et al, 2021) shows that most tools are tailored for human pangenomes and are not suited to bacteria which exhibit, among other characteristics, a larger variability. Such variability leads to the need for incorporating a greater flexibility when computing an alignment. In this paper, we extend the usual notion of sequence-to-graph alignment by including recombinations among the variations that explicitly represented and evaluated in an alignment. From a computational modeling point of view, a recombination corresponds to identifying a new path of the variation graph which is a mosaic of two different paths, possibly joined by a new arc. We provide a dynamic programming algorithm for computing an optimal alignment that allows recombinations with an affine penalty. We have implemented our approach with the tool RecGraph and we have analyzed its accuracy over some over some bacterial pangenome graphs.