deNOVOEnrich: Identification of de novo transposon insertion sites from targeted sequencing data

deNOVOEnrich is a computational pipeline developed to efficiently detect and profile genome-wide somatic transposition insertions, as well as non-reference heritable transposition events from targeted sequencing data generated through Transposon display sequencing (TEd-Seq). The pipeline leverages high-confidence split read alignments to identify TE: genome break sites, enabling accurate detection of bona-fide non-reference somatic and heritable new insertions of a transposon. Stringent filters were applied at several critical steps of the pipeline to ensure the removal of false positives and the reduction of background noise signal.This repository includes the source code for deNOVOEnrich and the input files required for detection of new transposon insertions from three transposon families in Arabidopsis - AtCOPIA78 (ONSEN), AtCOPIA93 (EVADE) and AtCOPIA21.