SOAPsv

SOAPsv is a tool for structural variant detection using short Illumina reads mapped to a reference genome. It has the capability of detecting homozygous structural variants (1-50 kb) that belong to category insertions, deletions, inversions and their precise breakpoints relative to a reference genome. It has been shown to have low false positive and false negative rates when compared to other similar methods.

Topic

Genetic variation

Detail

  • Operation: Structural variant analysis

  • Software interface: Command-line user interface

  • Language: C++;Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: zhangfanqw@gmail.com; liudongbing2@genomics.cn

  • Collection: -

  • Maturity: -

Publications

  • Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.
  • Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H, Ma H, Zhang F, Feng S, Zhang W, Du H, Tian G, Li J, Zhang X, Li S, Bolund L, Kristiansen K, de Smith AJ, Blakemore AI, Coin LJ, Yang H, Wang J, Wang J. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology. 2011;29(8): 723-30
  • https://doi.org/10.1038/nbt.1904
  • PMID: 21785424
  • PMC: -

Download and documentation

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