Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak.
Nat Commun
; 14(1): 283, 2023 01 17.
Article
em En
| MEDLINE
| ID: mdl-36650186
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 application of DeBreak is analyzing cancer genomes for potentially tumor-driving SVs. DeBreak can also be used for supplementing whole-genome assembly-based SV discovery.
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Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Genoma Humano
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article