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GSR: Simulator - HaploDX
| Attribute | Value |
|---|---|
| Title | HaploDX |
| Short Description | A python library to develop genomic data simulators |
| Long Description | The HaploDX library provides a collection of functions to generate simulated population-specific genomic data in VCF format. The library includes parameters and functions to control mutation rates, linkage disequilibrium strength and block lengths, and number of individuals. To generate genomic data, the HaploDX framework offers a pipeline of functions that can be used to simulate: (1) the allele frequency spectra of different populations; (2) the Hardy-Weinberg principle for genotypes and haplotypes; (3) linkage disequilibrium across different populations. |
| Keywords | GWAS, GWAS Dataset, Linkage Disequilibrium, VCF, Population Genomics, Population Genetics, Allele Frequency Spectrum, Hardy-Weinberg Equilibrium, Genomic Data, Microarray, SNP chips |
| Version | 0.4-beta.1 |
| Project Started | 2023 |
| Last Release | 2 years ago |
| Homepage | https://github.com/remytuyeras/HaploDynamics |
| Citations | Remy Tuyeras, How to simulate genomic data?, CTBCS Blog, March 3, 2023 [ Abstract ] |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Single Nucleotide Variation, Amino acid variation, |
| Simulation Method | Machine Learning, Other, |
| Input | |
| Data Type | Allele Frequencies, Saved simulation, Other, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Mutation, Linkage Disequilibrium, |
| Sequencing Reads | |
| File Format | VCF, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Bottleneck, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Two-allele Mutation Model, |
| Events Allowed | Varying Demographic Features, Varying Genetic Features, |
| Other | |
| Interface | Script-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using HaploDX has been provided.
Please propose new citations if you are aware of publications that use this software.