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 .

Cited by papers we hold 5

• Complex genetic variation in nearly complete human genomes · 2025
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• Detection of mosaic and population-level structural variants with Sniffles2 · 2024
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• Single-cell genomic variation induced by mutational processes in cancer · 2022
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• Graph pangenome captures missing heritability and empowers tomato breeding · 2022
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• PanSVR: Pan-Genome Augmented Short Read Realignment for Sensitive Detection of Structural Variations · 2021
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