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GenomeDelta: detecting recent transposable element invasions without repeat library
Genome Biology ( IF 10.1 ) Pub Date : 2024-12-18 , DOI: 10.1186/s13059-024-03459-5
Riccardo Pianezza, Anna Haider, Robert Kofler

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.

中文翻译:


GenomeDelta:检测近期无重复文库的转座因子侵袭



我们提出了 GenomeDelta,这是一种用于识别样品特异性序列的新型工具,例如最近的转座因子 (TE) 侵袭,而无需重复文库。GenomeDelta 将高质量组装与短读长数据进行比较,以检测短读长中缺失的序列。它适用于模式和非模式生物,可以识别最近的 TE 入侵、空间异质序列、病毒插入和热基因转移。GenomeDelta 使用模拟和真实数据进行了验证,并用于发现最近在黑腹果蝇中的三次 TE 入侵,以及在 Zymoseptoria tritici 中具有地理差异的新型 TE。
更新日期:2024-12-19
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