Transposable element detection from whole genome sequence data

The number of software tools available for detecting transposable element insertions from whole genome sequence data has been increasing steadily throughout the last ~5 years. Some of these methods have unique features suiting them for particular use cases, but in general they follow one or more of a common set of approaches. Here, detection and filtering approaches are reviewed in the light of transposable element biology and the current state of whole genome sequencing. We demonstrate that the current state-of-the-art methods still do not produce highly concordant results and provide resources to assist future development in transposable element detection methods.