axiomFP.py a software for visual ploidy and quality assessment of Axiom SNP array data
axiomFP.py is an open-source software developed to diagnose ploidy level and call quality for samples genotyped on Affymetrix Axiom SNP arrays by making frequency plots of normalized SNP call positions among SNPs meeting specific clustering parameters. This research outlines the methods employed in the development of the software, and presents the results obtained through its application on a dataset of mixed ploidy apple (Malus spp.) cultivars and germplasm accessions. The tools required to prepare the input files and operate the software are also described. The frequency plots generated by the software require a visual inspection to assess ploidy and call quality. The results have been validated using the available ploidy data, as well as flow cytometry, and have shown complete accuracy. The software is available on GitHub at https://github.com/allmiraria/axiomFP.