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, 5 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 (988 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.