GSR: Simulator - REGENS

Basic Package Attributes
AttributeValue
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 months, 4 weeks ago
Homepagehttps://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, 03-03-2021 [ Abstract ]
GSR Certification

Accessibility
Documentation
Application
Support

Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation MethodResample Existing Data,
Input
Data TypeReference genome,
File formatOther,
Output
Data TypeGenotype or Sequence, Phenotypic Trait,
Sequencing Reads
File FormatOther,
Sample TypeOther,
Phenotype
Trait TypeBinary or Qualitative, Quantitative,
DeterminantsMultiple 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
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguagePython,
LicenseOther,
GSR CertificationAccessibility, Documentation, Support,

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