VISOR (opens new window) 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 short (Illumina) and long (PacBio-ONT) reads sequencing data
- simulations of bulk and strand-seq sequencing data
- simulations of 10X linked reads sequencing data (BETA release)
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. All code is open-source and hosted on VISOR's GitHub page (opens new window).
Contents:
TIP
For questions, help or feature requests, please open an issue (opens new window) or get in touch with me at davidebolognini7@gmail.com
# Citation
Are you using VISOR in your works? Please cite:
Davide Bolognini, Ashley Sanders, Jan O Korbel, Alberto Magi, Vladimir Benes, Tobias Rausch. VISOR: a versatile haplotype-aware structural variant simulator for short and long read sequencing (opens new window). Bioinformatics. 2019 Oct 7.
# Related works
VISOR has been applied to simulate Strand-seq data in:
Ashley D Sanders, Sascha Meiers, Maryam Ghareghani, David Porubsky, Hyobin Jeong, M Alexandra CC van Vliet, Tobias Rausch, Paulina Richter-Pechańska, Joachim B Kunz, Silvia Jenni, Davide Bolognini, Gabriel MC Longo, Benjamin Raeder, Venla Kinanen, Jürgen Zimmermann, Vladimir Benes, Martin Schrappe, Balca R Mardin, Andreas E Kulozik, Beat Bornhauser, Jean-Pierre Bourquin, Tobias Marschall, Jan O Korbel. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing (opens new window). Nature Biotechnology. 2019 Dec 23.
VISOR has been applied to simulate repeat contractions/expansions in long-read data, as described in:
Davide Bolognini, Alberto Magi, Vladimir Benes, Jan O Korbel, Tobias Rausch. TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data (opens new window). GigaScience. 2020 Oct 7.
VISOR has been applied to simulate SVs in long-read data, as described in:
Davide Bolognini, Alberto Magi. Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data (opens new window). Front. Genet. 2021 Nov 18.