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GSR: Simulator - Mutation-Simulator
| Attribute | Value |
|---|---|
| Title | Mutation-Simulator |
| Short Description | Mutation-Simulator: fine-grained simulation of random mutations in any genome |
| Long Description | Mutation-Simulator allows the introduction of various types of sequence alterations in reference sequences, with reasonable compute-time even for large eukaryotic genomes. Its intuitive system for fine-grained control over mutation rates along the sequence enables the mimicking of natural mutation patterns. Using standard file formats for input and output data, it can easily be integrated into any development and benchmarking workflow for high-throughput sequencing applications. |
| Keywords | random mutation, sequence alterations, SNP, SV, genome simulation |
| Version | 3.0.1 |
| Project Started | 2020 |
| Last Release | 3 years, 2 months ago |
| Homepage | https://github.com/mkpython3/Mutation-Simulator |
| Citations | Kühl MA, Stich B, Ries DC, Mutation-Simulator: fine-grained simulation of random mutations in any genome., Bioinformatics, May 1, 2021 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Sept. 28, 2022 (934 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, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, VCF, |
| 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, Script-based, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | GNU Public License, |
| 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 Mutation-Simulator.
2023
Rigby C, Sabsay K, Bisht K, Eggink D, Jalal H, Te Velthuis AJW, Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes., bioRxiv, Aug. 2, 2023 [Abstract]
Arredondo-Alonso S, Gladstone RA, Pöntinen AK, Gama JA, Schürch AC, Lanza VF, Johnsen PJ, Samuelsen Ø, Tonkin-Hill G, Corander J, Mge-cluster: a reference-free approach for typing bacterial plasmids., NAR Genom Bioinform, July 10, 2023 [Abstract]