TEgenomeSimulator publication code

This repository contains the code to repoduce the analyses and figures presented in the publication of TEgenomeSimulator: A Flexible Framework for Simulating Genomes with Configurable Transposable Element Landscapes.

• The code for input file preperation, simulation, benchmarking and post-processing are in the folder script, with file extension sh or py.
• The code for generating figures used in the publication are in the folder script, with the file extension Rmd.
• The minimum input files (compressed), such as genome assemblies and TE libraries are stored in the folder input, unless the file size exceeds 100 Mb. Check input's README.md for details.
• To access the source code of the software TEgenomeSimulator, check its GitHub repository at https://github.com/Plant-Food-Research-Open/TEgenomeSimulator.