GSR: Simulator - VISOR

Basic Package Attributes
AttributeValue
Title VISOR
Short Description VISOR is a haplotype-aware structural variants simulator for short and long read sequencing
Long Description VISOR is an efficient and versatile command-line application, capable to simulate structural variants and small/single-nucleotide variants in a haplotype-resolved manner. VISOR currently supports simulations of bulk short (Illumina) and long (PacBio-ONT) reads sequencing data. VISOR also supports simulations of single cell, strand-seq data and includes a module, actively under development, capable to simulate 10X linked reads data. VISOR is readily applicable to canger genomics, enabling the simulation of tumour purity (normal in tumour contamination), heterogeneity (mix of several subclones) and aneuploidy. VISOR also incorporates capture biases, a crucial feature for whole-exome data sets and panel sequencing applications.
Keywords SV simulator short-reads long-reads strand-seq
Version 1.0
Project Started 2019
Last Release 1 year, 3 months ago
Homepagehttps://github.com/davidebolo1993/VISOR
Citations Bolognini D, Sanders A, Korbel JO, Magi A, Benes V, Rausch T, VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing., Bioinformatics, 02-15-2020 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated08-22-2019 (421 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 DataDiploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Sequencing Reads,
VariationsSingle Nucleotide Variation, Microsatellite, Insertion and Deletion, CNV, Inversion and Rearrangement,
Simulation MethodOther,
Input
Data Type
File format
Output
Data Type
Sequencing Reads
File FormatFasta 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
InterfaceCommand-line,
Development
Tested Platforms
LanguagePython,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Support,

The following 3 publications are selected examples of applications that used VISOR.

2020

Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, et al., Single-cell analysis of structural variations and complex rearrangements with tri-channel processing., Nat Biotechnol, 03-01-2020 [Abstract]

Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z, Liu Y, Liu B, Wang Y, Long-read-based human genomic structural variation detection with cuteSV., Genome Biol, 08-03-2020 [Abstract]

Bolognini D, Magi A, Benes V, Korbel JO, Rausch T, TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data., Gigascience, 10-07-2020 [Abstract]


Propose changes to this simulator