Overview of spacemake. (A) Spacemake can handle inputs from different spatial transcriptomics technologies. (B) Spacemake is able to handle any barcode strategy. Cell barcode and unique molecular identifier (UMI) lengths are variable, and their position can be on either read. (C) Preprocessing, qualuty control, and processing steps. Each sample is processed the same way, regardless of the input type. (D) Spacemake is modular and extendable. Each module is implemented with a separate set of rules and commands, and everything is assembled in a top-level Snakefile.