< i > KmerAperture < /i > : Retaining < i > k < /i > -mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes

by Matthew P. Moore, Mirjam Laager, Paolo Ribeca, Xavier Didelot By decomposing genome sequences intok-mers, it is possible to estimate genome differences without alignment. Techniques such ask-mer minimisers, for example 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. 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 ofk uniquek-mers per genome. On the other hand, contiguous series>k may be caused by accessory differences of lengthS-k+1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs withink bp from each other andKmerAperture can determine whether that is the case. To demonstrate use casesKmerAperture was 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, ...
Source: PLoS Genetics - Category: Genetics & Stem Cells Authors: Source Type: research