Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak.

ABSTRACT: Long-read sequencing has demonstrated great potential for characterizing all types of structural variations (SVs). However, existing algorithms have insufficient sensitivity and precision. To address these limitations, we present DeBreak, a computational method for comprehensive and accurate SV discovery. Based on alignment results, DeBreak employs a density-based approach for clustering SV candidates together with a local de novo assembly approach for reconstructing long insertions. A partial order alignment algorithm ensures precise SV breakpoints with single base-pair resolution, and a k-means clustering method can report multi-allele SV events. DeBreak outperforms existing tools on both simulated and real long-read sequencing data from both PacBio and Nanopore platforms. An important a

SUBMITTER: Chen Y 

PROVIDER: S-EPMC9845341 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature