GSR: Simulator - VarSim
Attribute | Value |
---|---|
Title | VarSim |
Short Description | A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications |
Long Description | VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing. |
Version | 0.8.6 |
Project Started | 2014 |
Last Release | 3 years, 5 months ago |
Homepage | https://github.com/bioinform/varsim |
Citations | Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY, VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications., Bioinformatics, 05-01-2015 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 04-24-2023 (333 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 | Genotype at Genetic Markers, |
Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, |
Simulation Method | Other, |
Input | |
Data Type | Reference genome, |
File format | Other, |
Output | |
Data Type | |
Sequencing Reads | |
File Format | VCF, |
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 | Windows, Mac OS X, Linux and Unix, |
Language | Python, |
License | BSD, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used VarSim.
2022
Rozhoňová H, Danciu D, Stark S, Rätsch G, Kahles A, Lehmann KV, SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing., Bioinformatics, 09-15-2022 [Abstract]
2021
Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, et al., CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing., Mol Ther Methods Clin Dev, 04-02-2021 [Abstract]