Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/davidebolo1993/VISOR

VarIant SimulatOR for short, long and linked reads
https://github.com/davidebolo1993/VISOR

Last synced: about 2 months ago
JSON representation

VarIant SimulatOR for short, long and linked reads

Host: GitHub
URL: https://github.com/davidebolo1993/VISOR
Owner: davidebolo1993
License: lgpl-3.0
Created: 2019-03-14T08:02:53.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2023-11-27T13:45:43.000Z (7 months ago)
Last Synced: 2023-11-27T14:34:03.597Z (7 months ago)
Language: Python
Homepage:
Size: 38.1 MB
Stars: 34
Watchers: 1
Forks: 10
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE.txt

Lists

awesome-linked-reads - VISOR - commit/davidebolo1993/VISOR?label=%20) (Tools)

README

# VISOR
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/visor/README.html)

![alt text](VISOR.png)

## VISOR: haplotype-aware structural variants simulator for short, long and linked reads

VISOR is available to be installed from source or as a [Docker container](https://hub.docker.com/r/davidebolo1993/visor).
Please have a look at [VISOR documentation](https://davidebolo1993.github.io/visordoc/) for any installation or usage questions.

[Source Code](https://github.com/davidebolo1993/VISOR/tree/master/VISOR)

[Documentation](https://davidebolo1993.github.io/visordoc/)

## 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](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btz719/5582674/). 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](https://www.nature.com/articles/s41587-019-0366-x). 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](https://academic.oup.com/gigascience/article/9/10/giaa101/5918863?searchresult=1). 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](https://doi.org/10.3389/fgene.2021.761791). Front. Genet. 2021 Nov 18.