ZANARDI: an open-source pipeline for multiple-species genomic analysis of SNP array data

Exploration of SNP array-based genomic data typically requires using specific software. However, the wide availability of analysis software brings extra challenges because of various degrees of user friendliness, a variety of installation and library requirements and dependence on many types of input file formats. The lack of conventions for common file formats hampers the possibility of streamlining analyses, resulting in making programming skills an essential pre-requirement for a successful genomic analysis. Here, we present zanardi, a tool designed to overcome the aforementioned obstacles in some high-profile SNP array-based data analyses. zanardi allows users to integrate multiple files from different formats, streamlining the study of population structure, data editing and/or other statistical analysis. Third-party software is integrated directly, so the user is required only to compile a parameter file and to run a simplified command-line command. Because all original options of the original third-party software can be included in the analysis, using zanardi does not reduce the flexibility of the single tools. zanardi is open source, and it was designed in modular form, thus it easily extendable to a larger number of analyses. Availability and implementation can be found at https://github.com/bioinformatics-ptp/Zanardi.git.