Fig. 1

Schematic of the OVERLAY computational pipeline. Boxed texts are files and data, where green rectangle, blue rectangle, and yellow diamond denote starting materials, intermediate steps, and results, respectively. Red italic texts refer to manual procedures, and purple italic texts refer to semi-manual steps with some script aids. In contrast, automatic procedures that are done by the only script are shown in green italic, and methods uniquely developed in OVERLAY are in bold green font