Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data.
Nakagome, M., Solovieva, E., Takahashi, A., Yasue, H., Hirochika, H., & Miyao, A. (2014). Transposon Insertion Finder (TIF): A novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics, 15(1). https://doi.org/10.1186/1471-2105-15-71