Abstract
Detection of transposition events of a transposon from short reads of next-generation sequencing (NGS) is challenging because transposons are repetitive and difficult to be distinguished from already existing transposons in the genome. Many transposons generate target site duplication (TSD) as the result of chromosomal integration. Since TSDs flanking the 5'-end (head) and 3'-end (tail) of a transposon has the identical sequences which are absent from the reference copy, the short reads containing the head or tail sequences of the transposon following the same TSD sequence may reveal the evidence of transposition. Transposon Insertion Finder (TIF) focuses on the TSD with flanking sequence of transposon and detects transposition events from NGS data. TIF software is available at https://github.com/akiomiyao/tif .
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