RAPTR-SV

RAPTR-SV is a software tool designed for the identification of structural variants (SVs) in sequence data with high sensitivity and precision. Simulations showed that RAPTR-SV had superior sensitivity and precision compared to other similar algorithms for SV detection. RAPTR-SV identified 66.4% of simulated tandem duplications with a precision of 99.2%, and when compared with calls made by Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications. The software is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications.

Topic

Whole genome sequencing;Genetics;DNA polymorphism

Detail

  • Operation: Genetic variation analysis

  • Software interface: Command-line user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: RAPTR-SV-v0.0.15

  • Credit: USDA CRIS, AFRI, USDA NIFA, the Agriculture and Food Research Initiative competitive grant, USDA National Institute of Food and Agriculture Animal Genome Program

  • Input: -

  • Output: -

  • Contact: Derek M. Bickhart derek.bickhart@ars.usda.gov

  • Collection: -

  • Maturity: -

Publications

  • RAPTR-SV: a hybrid method for the detection of structural variants.
  • Bickhart DM, et al. RAPTR-SV: a hybrid method for the detection of structural variants. RAPTR-SV: a hybrid method for the detection of structural variants. 2015; 31:2084-90. doi: 10.1093/bioinformatics/btv086
  • https://doi.org/10.1093/bioinformatics/btv086
  • PMID: 25686638
  • PMC: -

Download and documentation

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