ShRec3D: combining distance geometry and contact networks for a fast and easy 3D genome reconstruction from Hi-C data
external link: https://hal.archives-ouvertes.fr/hal-03172656
developed by Julien Mozziconacci (MNHN & LPTMC) and Annick Lesne (CNRS, LPTMC & IGMM)
ShRec3D is a network-based model-free algorithm for 3D genome reconstruction from Hi-C contact maps. This algorithm avoids convergence problems, accommodates sparse and noisy contact maps, and is orders of magnitude faster than existing methods. It is specially suitable for 3D visualization of genome annotations, e.g. chromatin epigenetic marks. The code is available in Matlab and Python.
Lesne A., Riposo J., Roger P., Cournac A., Mozziconacci J. (2014) 3D genome reconstruction from chromosomal contacts. Nature Methods 11, 1141. doi: 10.1038/nmeth.3104, https://hal.archives-ouvertes.fr/hal-02324120.
Carron L., Morlot J.B., Lesne A., Mozziconacci J. (2021) The 3D organization of chromatin colors in mammalian nuclei. Methods in Molecular Biology, vol. 2301, Hi-C Data Analysis: Methods and Protocols, Silvio Bicciato and Francesco Ferrari (eds. ISBN 978-1-0716-1389-4), Springer. https://hal.archives-ouvertes.fr/hal-03172656.
See also: J.B. Morlot, J. Mozziconacci, A. Lesne, Network concepts for analyzing 3D genome structure from chromosomal contact maps, European Physical Journal: Nonlinear Biomedical Physics 4, 2 (2016). doin: 10.1140/epjnbp/s40366-016-0029-5, https://hal.archives-ouvertes.fr/hal-03199686.