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GSR: Simulator - simuG
| Attribute | Value |
|---|---|
| Title | simuG |
| Short Description | simuG: a general-purpose genome simulator |
| Long Description | Simulated genomes with pre-defined or random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG as a light-weighted tool for simulating the full spectrum of genomic variants (SNPs, INDELs, CNVs, inversions, and translocations). In addition, simuG enables a rich array of fine-tuned controls, such as simulating SNPs in different coding partitions (e.g. coding sites, noncoding sites, 4-fold degenerate sites, or 2-fold degenerate sites); simulating CNVs with different formation mechanisms (e.g. segmental deletions, dispersed duplications, and tandem duplications); and simulating inversions and translocations with specific types of breakpoints. The simplicity and versatility of simuG make it a unique general purpose genome simulator for a wide-range of simulation-based applications. |
| Project Started | 2019 |
| Last Release | 4 years, 5 months ago |
| Homepage | https://github.com/yjx1217/simuG |
| Citations | Yue JX, Liti G, simuG: a general-purpose genome simulator., Bioinformatics, 11-01-2019 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 10-28-2021 (898 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 | Genotype at Genetic Markers, Diploid DNA Sequence, Sex Chromosomes, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Inversion and Rearrangement, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Other, |
| 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 | |
| Development | |
| Tested Platforms | |
| Language | |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used simuG.
2023
Yang Z, Guarracino A, Biggs PJ, Black MA, Ismail N, Wold JR, Merriman TR, Prins P, Garrison E, de Ligt J, Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads., Front Genet, 08-10-2023 [Abstract]
2022
Lefouili M, Nam K, The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species., Sci Rep, 07-05-2022 [Abstract]