phaidra.vetmeduni.ac.at o:3842 DOI 10.1186/s13059-024-03459-5 GenomeDelta: detecting recent transposable element invasions without repeat library 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. eng DNA Transposable Elements Animals Drosophila Melanogaster Genetics Software Ascomycota Genetics Gene Library 2025-02-03T15:45:48.627Z LOMv1.0 Author BEGIN:VCARD VERSION:3.0 N:Pianezza;Riccardo; FN:Riccardo Pianezza X-ORCID:https://orcid.org/0009-0007-6213-7853 END:VCARD BEGIN:VCARD VERSION:3.0 N:Haider;Anna; FN:Anna Haider END:VCARD BEGIN:VCARD VERSION:3.0 N:Kofler;Robert; FN:Robert Kofler X-ORCID:https://orcid.org/0000-0001-9960-7248 END:VCARD https://w3id.org/kim/hcrt/scheme https://w3id.org/kim/hcrt/text Textdokument Text LOMv1.0 yes https://creativecommons.org/licenses/by-nc-nd/4.0 application/pdf 2646298 https://phaidra.vetmeduni.ac.at/o:3842 https://phaidra.vetmeduni.ac.at/api/object/o:3842/thumbnail LOMv1.0 discipline