TEMP2 is a transposon-insertion-detecting algorithm. It can both detect germline insertions and estimate the number of de novo insertions for each transposon family.

You can find the code on our github page: https://github.com/weng-lab/TEMP2.

Please cite the following paper if you are using TEMP2 for transposon insertion detecting:
Yu et al. A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acid Research. 2021