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GSR: Simulator - PGsim
| Attribute | Value |
|---|---|
| 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 | 4 years, 4 months ago |
| Homepage | https://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 | ✔ Accessibility |
| Last evaluated | 09-30-2021 (926 days ago) |
| 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 | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | Reference genome, Other, |
| File format | Fstat, Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta 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 | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Perl, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using PGsim has been provided.
Please propose new citations if you are aware of publications that use this software.