Work

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

Year: 2025

Type: article

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://github.com/genomech/Charm): a robust computational framework tailored for Hi-C data simulation. Our findings demonstrate Charm's 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.

Source: NAR Genomics and Bioinformatics

DOI: 10.1093/nargab/lqaf081

Authors: Miroslav Nuriddinov, Polina Belokopytova, Veniamin Fishman

Institutions: Institute of Cytology and Genetics, Novosibirsk State University, Sirius University of Science and Technology, AIRI - Artificial Intelligence Research Institute

Language: English

Topic: Genomic variations and chromosomal abnormalities

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,766

Funders: Russian Science Foundation, Ministry of Science and Higher Education of the Russian Federation