An official website of the United States government
GSR: Simulator - VISOR
| Attribute | Value |
|---|---|
| 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 | 4 years, 9 months ago |
| Homepage | https://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 |
| Last evaluated | 08-22-2019 (1696 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 | Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Sequencing Reads, |
| Variations | Single Nucleotide Variation, Microsatellite, Insertion and Deletion, CNV, Inversion and Rearrangement, |
| Simulation Method | Other, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | Fasta 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 | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 7
The following 7 publications are selected examples of applications that used VISOR.
2023
Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, et al., Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures., Cell Genom, 03-22-2023 [Abstract]
2022
Duan X, Pan M, Fan S, Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data., BMC Genomics, 04-23-2022 [Abstract]
Chen Y, Miao Y, Bai W, Lin K, Pang E, Characteristics and potential functional effects of long insertions in Asian butternuts., BMC Genomics, 10-28-2022 [Abstract]
2021
Jiang T, Liu S, Cao S, Liu Y, Cui Z, Wang Y, Guo H, Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation., BMC Bioinformatics, 11-12-2021 [Abstract]
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]