This folder contains materials related to the publication of "Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis" in Communication Biology (Wang et al. 2024). These scripts includes the pipelines used for genome assembling and annotation. The intermediate steps are performed on different servers, thus, the data structure is quite messy. Credits for the scripts used for genome assembly and annotation go to Jarkko Salojärvi, Cui Wang, and Sitaram Rajaraman. If you would like to refer to this pipeline, please get familiar with the software used in the scripts, and customize it with your own folder structure.