Overview of an MPRA experiment with UMIs (top) and the MPRAsnakeflow pipeline for analyzing MPRA experiments (bottom). MPRAsnakeflow consists of an assignment workflow (left), which maps barcodes to designed oligos, and an experiment workflow (right), which counts barcodes and computes oligo activity. Inputs are shown in yellow, main processing steps in blue, and outputs in purple. Notably, MPRAsnakeflow supports different input read structures, including separate reads for oligo and barcode (A), as well as combined structures in which the barcode and oligo are present within read pairs (B). Reads can also be single-end reads.