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GSR: Simulator - REGENS
| Attribute | Value |
|---|---|
| Title | REGENS |
| Short Description | Simulates whole autosomes from real genomic segments in a way that preserves the input autosomes' linkage disequilibrium (LD) pattern. |
| Long Description | REGENS (REcombinatory Genome ENumeration of Subpopulations) is an open-source Python package that simulates whole genomes from real genomic segments. REGENS recombines these segments in a way that simulates completely new individuals while simultaneously preserving the input genomes' linkage disequilibrium (LD) pattern with extremely high fidelity. It takes plink (bed, bim, fam) file sets of existing genotype data as input and produces new (bed, bim, fam) file sets as output. REGENS can also simulate mono-allelic and epistatic single nucleotide variant (SNV) effects on a continuous or binary phenotype without perturbing the simulated LD pattern. REGENS was measured to be 88.5 times faster and require 6.2 times lower peak RAM on average than a similar algorithm called Triadsim. Our publication (https://doi.org/10.21105/joss.02743) and supplementary repository (https://github.com/EpistasisLab/regens-analysis) both contain more technical details. See our REGENS repository (REGENS repository (https://github.com/EpistasisLab/regens) for the source code, as well as detailed instructions and examples. |
| Keywords | gwas-tools, simulated-datasets |
| Version | v0.2.0c |
| Project Started | 2020 |
| Last Release | 4 years, 8 months ago |
| Homepage | https://github.com/EpistasisLab/regens/tags |
| Citations | John T. Gregg, Trang T. Le, Jason H. Moore, REGENS: an open source Python package for simulating realistic autosomal genotypes, JOSS, March 3, 2021 [ Abstract ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Sept. 28, 2022 (1058 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | |
| Variations | |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Reference genome, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, |
| Sequencing Reads | |
| File Format | Other, |
| Sample Type | Other, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, |
| Determinants | Multiple Genetic Markers, Gene-Gene Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Python, |
| License | Other, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using REGENS has been provided.
Please propose new citations if you are aware of publications that use this software.