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

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Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data. / Nuriddinov, Miroslav; Belokopytova, Polina ; Fishman, Veniamin.

In: NAR Genomics and Bioinformatics, Vol. 7, No. 2, lqaf081, 06.2025.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{14be6adf7075402e88b27b1892074b22,

title = "Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data",

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.",

author = "Miroslav Nuriddinov and Polina Belokopytova and Veniamin Fishman",

note = "We acknowledge the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to the computational facilities. The access to public resources and datasets was provided by the Novosibirsk State University, supported by the Ministry of Science and Higher Education of Russian Federation, grant FSUS-2024-0018. We thank Galina Koksharova for testing the Charm software. The study was supported by the grant of the state program of the \u201CSirius\u201D Federal Territory \u201CScientific and technological development of the \u2018Sirius\u2019 Federal Territory\u201D (agreement no. 26-03, 27/09/2024). Preliminary results were obtained with the financial support of the Russian Science Foundation, RSF (RSF grant # 22-14-00247). ",

year = "2025",

month = jun,

doi = "10.1093/nargab/lqaf081",

language = "English",

volume = "7",

journal = "NAR Genomics and Bioinformatics",

issn = "2631-9268",

publisher = "Oxford University Press",

number = "2",

}

RIS

TY - JOUR

T1 - Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data

AU - Nuriddinov, Miroslav

AU - Belokopytova, Polina

AU - Fishman, Veniamin

N1 - We acknowledge the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to the computational facilities. The access to public resources and datasets was provided by the Novosibirsk State University, supported by the Ministry of Science and Higher Education of Russian Federation, grant FSUS-2024-0018. We thank Galina Koksharova for testing the Charm software. The study was supported by the grant of the state program of the \u201CSirius\u201D Federal Territory \u201CScientific and technological development of the \u2018Sirius\u2019 Federal Territory\u201D (agreement no. 26-03, 27/09/2024). Preliminary results were obtained with the financial support of the Russian Science Foundation, RSF (RSF grant # 22-14-00247).

PY - 2025/6

Y1 - 2025/6

N2 - 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.

AB - 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.

UR - https://www.mendeley.com/catalogue/ccf84071-0346-3740-bb84-d4cb6de85418/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105008986720&origin=inward&txGid=7f8089be4c7b26c89356f5c1e6b88ced

U2 - 10.1093/nargab/lqaf081

DO - 10.1093/nargab/lqaf081

M3 - Article

C2 - 40585301

VL - 7

JO - NAR Genomics and Bioinformatics

JF - NAR Genomics and Bioinformatics

SN - 2631-9268

IS - 2

M1 - lqaf081

ER -

ID: 68177875