法国巴斯德研究所Rayan Chikhi等研究人员合作开发出新方法SVDSS，可实现在难以调用的基因组区域发现结构变异。相关论文于2022年12月22日在线发表在《自然—方法学》杂志上。

Title: SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads

Author: Denti, Luca, Khorsand, Parsoa, Bonizzoni, Paola, Hormozdiari, Fereydoun, Chikhi, Rayan

Issue&Volume: 2022-12-22

Abstract: Structural variants (SVs) account for a large amount of sequence variability across genomes and play an important role in human genomics and precision medicine. Despite intense efforts over the years, the discovery of SVs in individuals remains challenging due to the diploid and highly repetitive structure of the human genome, and by the presence of SVs that vastly exceed sequencing read lengths. However, the recent introduction of low-error long-read sequencing technologies such as PacBio HiFi may finally enable these barriers to be overcome. Here we present SV discovery with sample-specific strings (SVDSS)—a method for discovery of SVs from long-read sequencing technologies (for example, PacBio HiFi) that combines and effectively leverages mapping-free, mapping-based and assembly-based methodologies for overall superior SV discovery performance. Our experiments on several human samples show that SVDSS outperforms state-of-the-art mapping-based methods for discovery of insertion and deletion SVs in PacBio HiFi reads and achieves notable improvements in calling SVs in repetitive regions of the genome.

DOI: 10.1038/s41592-022-01674-1

Source: https://www.nature.com/articles/s41592-022-01674-1