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GSR: Simulator - Pysim-sv
| Attribute | Value |
|---|---|
| Title | Pysim-sv |
| Short Description | Pysim-sv: a package for simulating structural variation data with GC-biases |
| Long Description | Pysim-sv is a package for simulating HTS data to evaluate performance of SV detection algorithms. Pysim-sv can introduce a wide spectrum of germline and somatic genomic variations. The package contains functionalities to simulate tumor data with aneuploidy and heterogeneous subclones, which is very useful in assessing algorithm performance in tumor studies. Furthermore, Pysim-sv can introduce GC-bias, the most important and prevalent bias in HTS data, in the simulated HTS data. |
| Keywords | Breakpoints; Copy number variation; Next-generation sequencing; Translocation |
| Project Started | 2016 |
| Last Release | 8 years, 2 months ago |
| Homepage | https://github.com/xyc0813/pysim/ |
| Citations | Xia Y, Liu Y, Deng M, Xi R, Pysim-sv: a package for simulating structural variation data with GC-biases., BMC Bioinformatics, March 14, 2017 [ 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 | |
| Variations | Insertion and Deletion, CNV, |
| Simulation Method | |
| Input | |
| Data Type | Reference genome, |
| File format | SAM or BAM, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, SAM or BAM, |
| 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 | Script-based, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | |
| GSR Certification | Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Pysim-sv has been provided.
Please propose new citations if you are aware of publications that use this software.