Transposable elements (TEs) help shape the structure and function of the
human genome. When inserted into some locations, TEs may disrupt gene
regulation and cause diseases. Here, we present xTea (x-Transposable
element analyzer), a tool for identifying TE insertions in whole-genome
sequencing data. Whereas existing methods are mostly designed for
short-read data, xTea can be applied to both short-read and long-read data.
Our analysis shows that xTea outperforms other short read-based methods for
both germline and somatic TE insertion discovery. With long-read data, we
created a catalogue of polymorphic insertions with full assembly and
annotation of insertional sequences for various types of retroelements,
including pseudogenes and endogenous retroviruses. Notably, we find that
individual genomes have an average of nine groups of full-length L1s in
centromeres, suggesting that centromeres and other highly repetitive
regions such as telomeres are a significant yet unexplored source of active
L1s. xTea is available at https://github.com/parklab/xTea .
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