This is the code used to get a de novo repeat analysis using RepeatModeler2 on the wheatear genome, to get the repeat annotation using RepeatMasker and, finally, to get the associated figures for the paper "An annotated chromosome-scale reference genome for Eastern Black-eared Wheatear (Oenanthe melanoleuca)" Peona et al. 2022
All the analysis steps are in TE_characterisation_and_analysis.md
Required softwares are: RepeatModeler2, RepeatMasker, R version 4.1.1, R packages ggplot2, dplyr, data.table, Rcolorbrewer.