Abstract. A universal methodological approach has been developed that allows solving the problem of differentiating closely related species using raw NGS sequencing data. The method is based on the use of single nucleotide polymorphisms (SNPs). This approach is universal; it can be used in the bioinformatic analysis of sequencing results, regardless of the biological species under study. The approach we developed is based on automating the process of searching for nucleotide sequences flanking the desired allele. The search is carried out on the researcher's personal computer, does not require expensive equipment, the Python v.3.10 programming language and the Jupyter Notebook software development environment are free and publicly available. The methodological approach for in silico genotyping is implemented in the form of the GENIS software. Within the framework of this work, the program was tested on files with the results of genome sequencing of animals of the genus Sus. Revealed polymorphisms for the differentiation of pigs of the Duroc breed.