GSR: Simulator - PGsim

Basic Package Attributes
AttributeValue
Title PGsim
Short Description A Comprehensive and Highly Customizable Personal Genome Simulator
Long Description we designed and developed PGsim, a comprehensive and highly customizable individual genome simulator, that fully uses existing knowledge, such as variant allele frequencies in global or world main populations, mutation probability differences between protein-coding regions and non-coding regions, transition/transversion (Ti/Tv) ratios, Indel incidence, Indel length distribution, structural variation sites, and pathogenic mutation sites. Users can flexibly control the proportion and quantity of known variants, common variants, novel variants in both coding and non-coding regions, and special variants through detailed parameter settings. To ensure that the simulated personal genome has sufficient randomness, PGsim makes the generated variants more real and reliable in terms of variant distribution, proportion, and population characteristics. PGsim is able to employ a huge volume database as background data to simulate personal genomes and does not require SQL database support. Users can easily change the variant databases used as needed.
Version 1.0
Project Started 2019
Last Release 1 year, 9 months ago
Homepagehttps://github.com/lrjuan/PGsim
Citations Juan L, Wang Y, Jiang J, Yang Q, Jiang Q, Wang Y, PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator., Front Bioeng Biotechnol, 01-28-2020 [ Abstract, cited in PMC ]
GSR Certification This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation Method
Input
Data TypeReference genome, Other,
File formatFstat, Other,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatFasta or Fastq,
Sample Type
Phenotype
Trait Type
Determinants
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 Platforms
LanguagePerl,
LicenseMIT,
GSR Certification

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