Abstract
AbstractDetecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.
Publisher
Cold Spring Harbor Laboratory
Reference19 articles.
1. Genome structural variation discovery and genotyping
2. Chan, S. , Lam, E. , Saghbini, M. , Bocklandt, S. , Hastie, A. , Cao, H. , … Borodkin, M. (2018a). Structural variation detection and analysis using bionano optical mapping. In Copy number variants (pp. 193–203). Springer.
3. Chan, S. , Lam, E. , Saghbini, M. , Bocklandt, S. , Hastie, A. , Cao, H. , … Borodkin, M. (2018b). Structural variation detection and analysis using bionano optical mapping. In Copy number variants (pp. 193–203). Springer.
4. Connecting genome structural variation with complex traits in crop plants;Theoretical and applied genetics,2019
5. Genomics, B. (n.d.). Next-generation cytogenetics: Bionano whole genome mapping resolves structural variants in heterogeneous cancer samples.