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bioRxiv · 10.1101/2023.11.22.568374

Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.

Nuriddinov, M.·Fishman, V.·Belokopytova, P.
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Abstract

Identifying structural variants (SVs) remains a pivotal challenge within genomic studies. The recent advent of chromosome conformation capture (3C) techniques has emerged as a promising avenue for the accurate identification of SVs. However, development and validation of computational methods leveraging 3C data necessitate comprehensive datasets of well-characterized chromosomal rearrangements, which are presently lacking. In this study, we introduce Charm (https://zenodo.org/doi/10.5281/zenodo.10653353): a robust computational framework tailored for Hi-C data simulation. Our findings demonstrate Charms efficacy in benchmarking both novel and established tools for SV detection. Additionally, we furnish an extensive dataset of simulated Hi-C maps, paving the way for subsequent benchmarking endeavors.

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Nuriddinov, M., Fishman, V., Belokopytova, P.. 2023-11-23. Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.. https://doi.org/10.1101/2023.11.22.568374

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