Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Enhanced hg38 transposable element (TE) annotation and associated RepeatMasker outputs of hg38 chromosomes and reconstructed ancestral genomes (RAGs). Homo_sapiens_augmented.bed: Enhanced TE annotation in hg38 based on multiple RAGs. Homo_sapiens_RepeatMasker_out.tar.gz: RepeatMasker outputs of hg38 chromosomes. *.fa.out: RepeatMasker outputs of RAGs. halliftover.sh, merge.R, repeatmasker.sh, rm2bed.R: Scripts used to achieve enhanced TE annotation in hg38. *_ucsc_enhanced.bed: Enhanced TE annotation on UCSC-provided annotation based on the Eutherian RAG.