Thermofisher® Axiom genotype datasets for FruitBreedOmics domesticated apple samples, input files for the AxioSAFE data curation pipeline publication

AxioSAFE is a data curation pipeline which implements various curation steps on genetic markers, in particular SNPs, and samples present within an input genotyping dataset. AxioSAFE is designed to work with the specific format of genotype data exported through the proprietary Thermofisher® software (i.e., Axiom Analysis Suite, AxAS): the workflow of a genotyping experiment requires the usage of the proprietary software to run a Genotype Calling analysis on raw data generated through genotyping machines for the Axiom array technology platform. This upload provides a reference to the input files which were used in the original AxioSAFE article (reference pending) for data validation. Hereby are included data from Apple samples collected and analysed as part of the FruitBreedomics project. The original raw data was published in (Bianco et. al 2016) and courtesly made available by the authors of the original paper. AxAS was run on the raw data with a "Best Practices Workflow" genotype calling operation, and the data was then export with its Export functionality. Basic documentation on how to use AxAS to export the data required by AxioSAFE is included in the AxioSAFE repository. References: AxioSAFE data curation pipeline: repository https://bitbucket.org/lzspin/axiosafe/src/master/, DockerHUB page https://hub.docker.com/r/lzspin/axiosafe Bianco, Luca, Alessandro Cestaro, Gareth Linsmith, et al. 2016. ‘Development and Validation of the Axiom ® Apple480K SNP Genotyping Array’. The Plant Journal 86 (1): 1. https://doi.org/10.1111/tpj.13145.