GSR: Simulator - XomeBlender

Basic Package Attributes
AttributeValue
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
Homepagehttps://github.com/rsemeraro/XomeBlender
Citations
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated05-11-2021 (132 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsCNV,
Simulation MethodResample Existing Data,
Input
Data TypeEmpirical,
File format
Output
Data TypeGenotype or Sequence,
Sequencing ReadsIllumina,
File FormatSAM or BAM,
Sample TypeRandom 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
InterfaceCommand-line,
Development
Tested Platforms
LanguageR, Python,
LicenseGNU Public License,
GSR CertificationAccessibility, 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]


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