SDFA: A Standardized Decomposition Format and Toolkit for Efficient Analysis of Structural Variants in Large-scale Population Genomic Studies Article Swipe
Wenjie Peng
,
Liubin Zhang
,
Bin Tang
,
Junhao Liang
,
Zhi Liu
,
Lihang Ye
,
Yangyang Yuan
,
Yifei Wang
,
Rui Tan
,
Nan Lin
,
Chao Xue
,
Hui Jiang
,
Fang Li
,
Miaoxin Li
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-5058112/v1
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-5058112/v1
Structural variants (SVs) contribute significantly to genetic diversity yet present computational challenges during analysis. We introduce SDFA, a standardized decomposition format and toolkit for efficient analysis of SVs in large-scale population genomics. SDFA efficiently stores and retrieves all SV types while providing algorithms for consistent SV merging, memory-efficient annotation, and precise gene feature annotation across large cohorts. SDFA outperforms existing tools, achieving at least 17.64 times faster merging and 120.93 times faster annotation, and uniquely handles complex SVs. We validate SDFA on 895,054 SVs from 150,119 individuals in the UK Biobank dataset.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-5058112/v1
- https://www.researchsquare.com/article/rs-5058112/latest.pdf
- OA Status
- gold
- References
- 46
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4410760692
All OpenAlex metadata
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- DOI
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https://doi.org/10.21203/rs.3.rs-5058112/v1Digital Object Identifier
- Title
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SDFA: A Standardized Decomposition Format and Toolkit for Efficient Analysis of Structural Variants in Large-scale Population Genomic StudiesWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-05-27Full publication date if available
- Authors
-
Wenjie Peng, Liubin Zhang, Bin Tang, Junhao Liang, Zhi Liu, Lihang Ye, Yangyang Yuan, Yifei Wang, Rui Tan, Nan Lin, Chao Xue, Hui Jiang, Fang Li, Miaoxin LiList of authors in order
- Landing page
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https://doi.org/10.21203/rs.3.rs-5058112/v1Publisher landing page
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https://www.researchsquare.com/article/rs-5058112/latest.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.researchsquare.com/article/rs-5058112/latest.pdfDirect OA link when available
- Concepts
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Decomposition, Scale (ratio), Computational biology, Population, Computer science, Biology, Geography, Cartography, Demography, Sociology, EcologyTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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46Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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