The PVY strainer workflow allows for determining the origin of recombinant sequence regions from non-recombinant PVY strains. In the first step, two PVY strains are aligned using the ClustalW program to standardize nucleotide positions, and a k-mer database is created with gmer_counter, excluding k-mers that are present in both strains or contain deletions in either strain. In the second step, the frequencies of the k-mers from the gmer_counter database are counted in the HTS data, and based on these frequencies, a visual graph is generated using an R script, either by strain subset or sequencing depth. This workflow can also be used with other sequences that are clearly divided into two or more groups.