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Long-read-based human genomic structural variation detection with cuteSV.

ABSTRACT: Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high yields and performance simultaneously due to the complex SV signatures implied by noisy long reads. We propose cuteSV, a sensitive, fast, and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to implement sensitive SV detection. Benchmarks on simulated and real long-read sequencing datasets demonstrate that cuteSV has higher yields and scaling performance than state-of-the-art tools. cuteSV is available at https://github.com/tjiangHIT/cuteSV .

SUBMITTER: Jiang T

PROVIDER: S-EPMC7477834 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Long-read-based human genomic structural variation detection with cuteSV.

Jiang Tao T Liu Yongzhuang Y Jiang Yue Y Li Junyi J Gao Yan Y Cui Zhe Z Liu Yadong Y Liu Bo B Wang Yadong Y

Genome biology 20200803 1

Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high yields and performance simultaneously due to the complex SV signatures implied by noisy long reads. We propose cuteSV, a sensitive, fast, and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to implement sensitive SV detection. ...[more]

PMID: 32746918

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