https://phaidra.vetmeduni.ac.at/o:3842 GenomeDelta: detecting recent transposable element invasions without repeat library Pianezza, Riccardo Riccardo Pianezza 0009-0007-6213-7853 University of Veterinary Medicine Vienna Haider, Anna Anna Haider University of Veterinary Medicine Vienna Kofler, Robert Robert Kofler 0000-0001-9960-7248 University of Veterinary Medicine Vienna BMC journal article open access eng We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici. DNA Transposable Elements Animals Drosophila Melanogaster Genetics Software Ascomycota Genetics Gene Library http://creativecommons.org/licenses/by-nc-nd/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:3842/download 10.1186/s13059-024-03459-5 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Genome Biology issn:1474-760X VoR Genome Biology 25 1 2.52 MB 2024