AxioSAFE: an accessible, semi-automatic filtering tool for the curation of genotyping datasets

Motivation Genotyping datasets generated via the Thermo Fisher Axiom® array are generally big, as they comprise tens of thousands of markers and hundreds of individuals, and currently, no automatic data curation pipelines are available for this kind of data. This leaves researchers with only time-consuming manual analysis as the current standard for processing these complex genotyping datasets. There is a clear need for a more efficient, streamlined approach to handle the specific quality control challenges inherent in this platform. Results AxioSAFE (Axiom SNP Assessment and Filtering Engine) is a semi-automatic computer tool for the curation of single nucleotide polymorphism (SNP) genotyping datasets generated via Thermo Fisher Axiom® array experiments. AxioSAFE provides an alternative methodology to cover a set of data curation operations, including steps such as a ploidy check, SNP filtering, Mendelian error analysis, and phasing. AxioSAFE identifies major occurrences of problematic SNPs and samples, including those not caught by the Axiom array default QC filters. Further functionality is included to let the user review identified problematic SNP classes. Availability and implementation AxioSAFE is a Python program that can be either used via the command line interface or through a graphical user interface (GUI) and is provided as a Docker container available on DockerHub at https://hub.docker.com/r/lzspin/axiosafe, which includes all required libraries, software, and a tutorial dataset. The source code and documentation are available at https://bitbucket.org/lzspin/axiosafe/. The apple dataset used for the development of AxioSAFE is available at DOI: https://doi.org/10.5281/zenodo.18034024