GSR: Simulator - SCSIM

Basic Package Attributes
AttributeValue
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
Homepagehttps://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 ]
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Last evaluatedAug. 5, 2022 (988 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 DataSingle-Cell Sequencing, Bulk Sequencing,
Variations
Simulation Method
Input
Data TypeReference genome,
File format
Output
Data Type
Sequencing Reads
File FormatFasta 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
InterfaceCommand-line,
Development
Tested Platforms
LanguagePython,
LicenseMIT,
GSR CertificationAccessibility, Documentation, Support,

Number of Primary Citations: 1

Number of Non-Primary Citations: 0

No example publication using SCSIM has been provided.

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