What’s the STARK?

sc3DG-seq has emerged as an essential tool for understanding the variability in 3D chromatin structure among individual cells. The process encompasses cell sorting, chromosome cross-linking, digestion, ligation, and sequencing, culminating in a map of interactions across the genome. Despite the development of over ten distinct sc3DG-seq techniques, each with unique processing requirements, a unified computational framework has been lacking. This gap poses a significant challenge to the research community, hindering the effective utilization of these extensive and valuable data.

To address this challenge, we propose STARK, a unified framework that conducts preprocessing, quality control and downstream analysis for all current sc3DG-seq data types (Fig S1). STARK encompasses three modules: Preprocess, Cell QC (Quality Control) and Downstream Analysis.

STARK is a software for processing various types of sc3DG-seq sequencing data, which currently includes the sc3DG-seq technologies as follows:

• scHi-C (Nagano et al., 2013)

• scHi-C+ (Argelaguet et al., 2019)

• Dip-C (Tan et al., 2018)

• HiRES (Wang et al., 2023)

• sn-m3C (Lee et al., 2019)

• scSPRITE (Quinodoz et al., 2018)

• sciHi-C (Ramani et al., 2017)

• snHi-C (Lee et al., 2019)

• scNanoHi-C (Lee et al., 2022)

• scMethyl-HiC (Li et al., 2019)