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

• Main Authors: Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu, Yadong Wang
• Format: Article
• Language: English
• Published: BMC 2020-08-01
• Series: Genome Biology
• Subjects: Structural variants detection; Long-read sequencing; Scaling performance
• Online Access: http://link.springer.com/article/10.1186/s13059-020-02107-y

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 .