SVbyEye <img src="man/figures/SVbyEye_online.png" align="right"/>

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R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

Author: David Porubsky

Installation

Development version from Github

To install the development version from Github, follow the steps given below. The installation has only been tested on Linux (Ubuntu) system, if you need to install on Windows or Mac-OS additional steps might be necessary.

1. Install a recent version of R (>=4.3) from https://www.r-project.org/
   Under Linux make sure current version of r-base & r-base-dev is installed.
   Under Windows it is recommended to install recent version of Rtools from https://cran.r-project.org/bin/windows/Rtools/\
2. Optional: For ease of use, install Rstudio from https://www.rstudio.com/
3. Open R or RStudio and execute the following lines one by one (Please ensure that you have writing permissions to install packages):

## Install required packages
install.packages("devtools")
library(devtools)

## Install from GitHub repository
devtools::install_github("daewoooo/SVbyEye", branch="master")

Documentation

See here for a detailed package usage.

Report Errors

If you encounter errors of any kind or want to request a new package functionality, please report an issue here.

Citation

Porubsky, David, Xavi Guitart, Dongahn Yoo, Philip C. Dishuck, William T. Harvey, and Evan E. Eichler. 2024. “SVbyEye: A Visual Tool to Characterize Structural Variation among Whole-Genome Assemblies.” bioRxiv. https://doi.org/10.1101/2024.09.11.612418.