Summary: ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. Availability and implementation: ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R.