ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments Authors
Abstract
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.
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BibTeX
@article{mendiboure2026sshicstuff,
title = {{ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments Authors}},
author = {Nicolas Mendiboure and Laurent Modolo and Stéphane Janczarski and Aurèle Piazza},
journal = {Bioinformatics},
year = {2026},
month = jun,
doi = {10.1093/bioinformatics/btag417},
url = {https://hal.science/hal-05760171v1},
note = {CC BY-SA 4.0},
}
RIS
TY - JOUR
TI - ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments Authors
AU - Nicolas Mendiboure
AU - Laurent Modolo
AU - Stéphane Janczarski
AU - Aurèle Piazza
PY - 2026
DA - 2026/06/22
JO - Bioinformatics
DO - 10.1093/bioinformatics/btag417
UR - https://hal.science/hal-05760171v1
AB - 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.
SN - 1367-4803
SN - 1367-4811
ER -