ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments

Single-strand DNA-specific Hi-C (ssHi-C) is a recently developed technique enabling the capture of chromatin interactions involving single-stranded DNA (ssDNA), an intermediate of various DNA metabolic processes. ssHi-C entails the restoration of restriction sites in ssDNA regions of interest upon introduction of designer, internally barcoded "annealing oligonucleotides" prior to the restriction digestion step of Hi-C. The design of these "annealing oligonucleotides," as well as the analysis of the resulting ssHi-C data presents specific challenges, such as (i) differentiating ssDNA from dsDNA-derived contacts, (ii) tracking probe-specific interactions, and (iii) calibrating the amount of ssDNA contacts across biological samples. Dedicated computational tools are therefore needed to facilitate the design of, and extract biological information from, ssHi-C experiments.

We present ssHiCstuff, a Rust- and Python-based package for the design of key reagents for ssHi-C experiments and for the analysis of ssHi-C data. ssHiCstuff provides (i) an automated annealing oligonucleotides design module, (ii) an end-to-end analyses pipeline, and (iii) a graphical user interface. ssHiCstuff simplifies the high-resolution analysis of ssDNA interactions at genome-wide scale. A graphical user interface (GUI) implemented in Python is also available for biologists without coding skills.

ssHiCstuff is freely available at https://github.com/Piazzalab/ssHiCstuff and https://zenodo.org/records/19677479 (https://doi.org/10.5281/zenodo.19677479) under the GPL 3.0 license. The annealing oligonucleotides design and the visualization modules are additionally freely available on a web browser at https://bioshiny.ens-lyon.fr/public/app/sshicstuff. A test dataset is available at https://zenodo.org/records/20035366 (https://doi.org/10.5281/zenodo.20035366).