Harmonizing single-cell 3D genome data with STARK and scNucleome

Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, quality control, and analysis of diverse sc3DG-seq data. Utilizing STARK, we benchmark 15 technologies, quantitatively comparing their strengths and limitations. We also develop EmptyCells to filter empty barcodes and introduce Spatial Structure Capture Efficiency (SSCE) to assess chromatin structure capture quality. Additionally, we establish scNucleome, a uniformly processed repository of sc3DG-seq datasets, to serve as a foundational resource for future 3D genome research.