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

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ID: 318186
2026
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Abstract
Abstract Motivation 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. Results 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. Availability ssHiCstuff is freely available at https://github.com/Piazzalab/ssHiCstuff and https://zenodo.org/records/19677479 (doi: 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 (doi: https://doi.org/10.5281/zenodo.20035366).
Reference Key
openalex_W7165541636 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Nicolas Mendiboure, Laurent Modolo, Stéphane Janczarski, Aurèle Piazza
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag417
URL
https://doi.org/10.1093/bioinformatics/btag417
Keywords Keywords not found

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