Extensive de-novo TE Annotator

Earl Grey: A fully automated TE curation and annotation pipeline

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

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

High-precision TE Annotator

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).

Annotation helper tool for the manual curation of transposable element consensus sequences

MCHelper: An automatic tool to curate transposable element libraries

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4

A toolkit for annotation of transposable element families from unassembled sequence reads

A tool for discovering transposable elements and describing patterns of genome evolution

starfish: a modular toolkit for giant mobile element annotation

Distribution of TEs and their relationship to genes in host genome

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

Transposon Insertion Finder - Detection of new TE insertions in NGS data

Genotyping of segregating mobile elements insertions

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

Snakemake pipeline to analyze transposable element 'omics data.

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

Nextflow workflow for automatic repeat detection, classification and masking