GSR: Simulator - XomeBlender
| Attribute | Value |
|---|---|
| Title | XomeBlender |
| Short Description | Generates synthetic cancer genomes with different contamination level and intra-tumor heterogeneity and devoid of any synthetic element |
| Long Description | Xome-Blender is a collection of python and R scripts based on SAMtools functions that allows to generate synthetic cancer genomes with user defined features such as the number of subclones, the number of somatic variants and the presence of CNV, without the addition of any synthetic element. It is composed of two modules: InXalizer and Xome-Blender. The first module is devoted to the blending process initialization. It takes as input a single BAM file, a set of user-defined parameters and returns the coverage of the sample and the input-files for the second module (Xome-Blender). Optionally, it creates a file containing the coordinates to insert CNV in the final product. The second module generates the synthetic heterogeneous sample. |
| Version | 3.1 |
| Last Release | 1 year ago |
| Homepage | https://github.com/rsemeraro/XomeBlender |
| Citations | |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 05-11-2021 (132 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 | Haploid DNA Sequence, |
| Variations | CNV, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Empirical, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | Illumina, |
| File Format | SAM or BAM, |
| Sample Type | Random or Independent, |
| 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 | R, Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Support, |
The following 1 publications are selected examples of applications that used XomeBlender.
2018
Semeraro R, Orlandini V, Magi A, Xome-Blender: A novel cancer genome simulator., PLoS One, 04-05-2018 [Abstract]