Top 6 transposable-elements open source projects

Earl Grey: A fully automated TE curation and annotation pipeline

Genotyping of segregating mobile elements insertions

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

Extensive de-novo TE Annotator

Distribution of TEs and their relationship to genes in host genome