The Contribution of Retrotransposons to Canine Genome Variation

We annotated common repeats in the UU_Cfam_GSD_1.0 canine reference genome derived from a German Shepherd Dog (GCA_011100685.1, canFam4) using RepeatMasker (version 4.2.4, using a merged database made from the Dfam curated consensus version 4.0 and RepBase RepeatMasker edition 20181026 sequences with the option -species dog) using the rmblastn aligner (version 2.9.0+) (215-217). To get a more accurate count of individual elements, we merged fragmented entries using the parseRM_merge_interrupted.pl script from https://github.com/4ureliek/Parsing-RepeatMasker-Outputs.