KmerAperture: Retainingk-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes

ABSTRACTBy decomposing genome sequences intok-mers, it is possible to estimate genome differences without alignment. Techniques such ask-mer minimisers (MinHash), have been developed and are often accurate approximations of distances based on fullk-mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment or mapping. However, thesek-mer set comparisons are not entirely accurate within-species and can be completely inaccurate within-lineage. This is due, in part, to their inability to distinguish core polymorphism from accessory differences. Here we present a new approach,KmerAperture, which uses information on thek-mer relative genomic positions to determine the type of polymorphism causing differences ink-mer presence and absence between pairs of genomes. Single SNPs are expected to result in contiguous series of relative uniquek-mers of lengthL=k. On the other hand, series of lengthL>kmay be caused by accessory differences of lengthL-k+1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs withinkbp from each other andKmerAperturecan determine whether that is the case. To demonstrate use casesKmerAperturewas benchmarked using datasets including a very low diversity simulated population with accessory content independent from the number of SNPs, a simulated population were SNPs are spatially dense, a moderately diverse real cluster of genomes (Escherichia coliST1193) with a large accessory genome and a low diversity real genome cluster (SalmonellaTyphimurium ST34). We show thatKmerAperturecan accurately distinguish both core and accessory sequence diversity without alignment, outperforming otherk-mer based tools.