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PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing. PoPoolation TE calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions.
PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences .
Documentation: https://sourceforge.net/p/popoolationte/wiki/Main/
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