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

Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV signatures implied by noisy long reads. Therefore, 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 analyze the signatures to implement sensitive SV detection. Benchmarks on real PacBio and ONT datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV is available at https://github.com/tjiangHIT/cuteSV.