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GSR: Simulator - SCSIM
| Attribute | Value |
|---|---|
| Title | SCSIM |
| Short Description | SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data |
| Long Description | SCSIM simulates DNA sequencing data from hierarchically grouped (correlated) samples where each sample is designated bulk or single-cell. Our tool uses a simple configuration file to define the experimental arrangement and can be integrated into software pipelines for testing of variant callers or other genomic tools. |
| Keywords | DNA sequencing; Hierarchical Dirichlet; Single-cell DNA sequencing; simulator |
| Project Started | 2019 |
| Last Release | 5 years, 6 months ago |
| Homepage | https://github.com/flahertylab/scsim |
| Citations | Giguere C, Dubey HV, Sarsani VK, Saddiki H, He S, Flaherty P, SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data., BMC Bioinformatics, May 26, 2020 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Aug. 5, 2022 (1112 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 | Single-Cell Sequencing, Bulk Sequencing, |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | Reference genome, |
| File format | |
| Output | |
| Data Type | |
| 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 | Python, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SCSIM has been provided.
Please propose new citations if you are aware of publications that use this software.