Harpy is a command-line tool to easily process platform-agnostic linked-read or WGS data. It uses Snakemake under the hood to execute different workflows (quality control, trimming, alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, and reproducibility, Harpy quickly handles data processing so that you can focus more on analyzing your data.