Title (eng)
GenomeDelta: detecting recent transposable element invasions without repeat library
Abstract (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.
Keywords (eng)
DNA Transposable ElementsAnimalsDrosophila Melanogaster GeneticsSoftwareAscomycota GeneticsGene Library
Type (eng)
Language
[eng]
Persistent identifier
Is in series
Title (eng)
Genome Biology
Volume
25
Issue
1
ISSN
1474-760X
Issued
2024
Number of pages
16
Publication
BMC
Version type (eng)
Date issued
2024
Access rights (eng)
License
Rights statement (eng)
© 2024. The Author(s).
- Citable links
Persistent identifier
DOI
https://phaidra.vetmeduni.ac.at/o:3842
https://doi.org/10.1186/s13059-024-03459-5 - Content
- DetailsObject typePDFDocumentFormatapplication/pdfCreated03.02.2025 03:45:48 UTC
- Usage statistics--
- This object is in collection
- Metadata
- Export formats