ALCHEMY

ALCHEMY is a genotype calling algorithm that uses statistical modeling of raw intensity data instead of clustering, making it suitable for small sample sizes and accurate genotyping of both inbred and heterozygous samples. It estimates and incorporates inbreeding information on a per-sample basis, and its accuracy exceeds 99% with as few as 18 samples.

Topic

Genotype and phenotype;DNA polymorphism;Genetics

Detail

  • Operation: Genotyping

  • Software interface: Command-line user interface

  • Language: C

  • License: GNU General Public License, version 3

  • Cost: Free

  • Version name: 1.07

  • Credit: United States National Science Foundation

  • Input: -

  • Output: -

  • Contact: Mark H. Wright mhw6@cornell.edu

  • Collection: -

  • Maturity: -

Publications

  • ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.
  • Wright MH, et al. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. 2010; 26:2952-60. doi: 10.1093/bioinformatics/btq533
  • https://doi.org/10.1093/bioinformatics/btq533
  • PMID: 20926420
  • PMC: PMC2982150

Download and documentation

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