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linkSNPs

linkSNPs

A tool to detect single nucleotide polymorphism (SNP) and to reconstruct haplotypes of a diploid organism, i.e., it can identify SNPs originating from each parent. The linkSNPs algorithm requires, on average, five heterozygous sites per kilobase of sequence.

Topic

Genetics; DNA polymorphism

Details

  • Operation: SNP detection; haplotype mapping
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.2
  • Maturity: Stable
  • Credit: -
  • Contact: innan_hideki _at_ soken.ac.jp | eriko.sasaki _at_ gmi.oeaw.ac.at
  • Collection: -

Publications

Sasaki E, Sugino RP, Innan H "The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data." Mol Biol Evol. 2013 Sep;30(9):2187-96. 31. https://doi.org/10.1093/molbev/mst103
PMID: 23728796


Download and documentation




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