Smudgeplot is a bioinformatics CLI tool for reference-free ploidy inference from whole genome sequencing data. It operates on FastK k-mer databases, identifying heterozygous k-mer pairs (hetmers) using a high-performance C backend, then aggregates them into 'smudges' via a local clustering algorithm in Python. The tool infers haploid coverage through a grid search and produces 2D histogram plots (smudgeplots) that reveal haplotype structure. The codebase is a hybrid of a Python package (command-line interface, data analysis, matplotlib-based visualization) and a custom C library (parallelized k-mer pair detection). It follows a clean architecture with well-separated concerns, a comprehensive CLI, and CI/CD pipelines for distribution. The project is actively maintained, with recent support for Python 3.14 and cross-platform wheel builds.