1. PerSVade: personalized structural variant detection in any species of interest
- Author
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Miquel Àngel Schikora-Tamarit, Toni Gabaldón, and Barcelona Supercomputing Center
- Subjects
Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC] ,DNA Copy Number Variations ,Genome, Human ,High-Throughput Nucleotide Sequencing ,Genomics ,Benchmarking ,Eukaryotic cell genetics ,Parameter optimization ,Simulació per ordinador ,Genomic Structural Variation ,Variant calling ,Humans ,Short reads ,Structural variants ,Algorithms - Abstract
Structural variants (SVs) underlie genomic variation but are often overlooked due to difficult detection from short reads. Most algorithms have been tested on humans, and it remains unclear how applicable they are in other organisms. To solve this, we develop perSVade (personalized structural variation detection), a sample-tailored pipeline that provides optimally called SVs and their inferred accuracy, as well as small and copy number variants. PerSVade increases SV calling accuracy on a benchmark of six eukaryotes. We find no universal set of optimal parameters, underscoring the need for sample-specific parameter optimization. PerSVade will facilitate SV detection and study across diverse organisms.
- Published
- 2022