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

ABSTRACT: By decomposing genome sequences into k-mers, it is possible to estimate genome differences without alignment. Techniques such as k-mer minimisers, for example MinHash, have been developed and are often accurate approximations of distances based on full k-mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment. However, these k-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 the k-mer relative genomic positions to determine the type of polymorphism causing differences in k-mer presence and absence betwe

SUBMITTER: Moore MP 

PROVIDER: S-EPMC11101094 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature