Comparison of multiple algorithms to reliably detect structural variants in pears

BACKGROUND: Structural variations (SVs) have been reported to play an important role in genetic diversity and trait regulation. Many computer algorithms detecting SVs have recently been developed, but the use of multiple algorithms to detect high-confidence SVs has not been studied. The most suitable sequencing depth for detecting SVs in pear is also not known. RESULTS: In this study, a pipeline to detect SVs using next-generation and long-read sequencing data was constructed. The performances of seven types of SV detection software using next-generation sequencing (NGS) data and two types of software using long-read sequencing data (SVIM and Sniffles), which are based on different algorithms, were compared. Of the nine software packages evaluated, SVIM identified the most SVs, and Sniffles detected SVs with the highest accuracy (> 90%). When the results from multiple SV detection tools were combined, the SVs identified by both MetaSV and IMR/DENOM, which use NGS data, were more accurate than those identified by both SVIM and Sniffles, with mean accuracies of 98.7 and 96.5%, respectively. The software packages using long-read sequencing data required fewer CPU cores and less memory and ran faster than those using NGS data. In addition, according to the performances of assembly-based algorithms using NGS data, we found that a sequencing depth of 50× is appropriate for detecting SVs in the pear genome. CONCLUSION: This study provides strong evidence that more than one SV detection software package, each based on a different algorithm, should be used to detect SVs with higher confidence, and that long-read sequencing data are better than NGS data for SV detection. The SV detection pipeline that we have established will facilitate the study of diversity in other crops.