SKSV: ultrafast structural variation detection from circular consensus sequencing reads

• DOI: 10.1093/bioinformatics/btab341
• Publication Date: 2021-05-04T12:14:13Z
• Authors: Yadong Liu; Tao Jiang; Junhao Su; Bo Liu; Tianyi Zang; Yadong Wang
• Keywords: Structural Variation; Variation (astronomy)

Circular consensus sequencing reads are promising for the comprehensive detection of structural variants (SVs). However, alignment-based SV calling pipelines computationally intensive due to generation complete read-alignments and its post-processing. Herein, we propose a SKeleton-based analysis toolkit Structural Variation (SKSV). Benchmarks on real simulated datasets demonstrate that SKSV has an order magnitude faster speed than state-of-the-art approaches; moreover, it achieves higher F1 scores various types SVs.SKSV is available from https://github.com/ydLiu-HIT/SKSV.Supplementary data at Bioinformatics online.