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Transposable element identification software tools | Pool sequencing data analysis

Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking.

Source text:
(Kofler et al., 2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet.

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LoRTE / Long Read Transposable Element
Identifies transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements (TEs) using low coverage, long read sequences. We demonstrated that LoRTE performs well even at low coverage PacBio read providing a cost effective tool to study the dynamics and impact of TEs in natural populations.
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