Extensive de-novo TE Annotator

• UpdatedOct 12, 2025
• Perl

Earl Grey: A fully automated TE curation and annotation pipeline

• UpdatedFeb 12, 2026
• Python

High-precision TE Annotator

• UpdatedDec 4, 2025
• Python

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

• UpdatedJul 4, 2025
• Python

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

• UpdatedJan 26, 2023
• Jupyter Notebook

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).

• UpdatedMar 29, 2023
• Dockerfile

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

• UpdatedMar 5, 2025
• R

MCHelper: An automatic tool to curate transposable element libraries

• UpdatedJul 3, 2025
• Python

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

• UpdatedSep 30, 2024
• Python

starfish: a modular toolkit for giant mobile element annotation

• UpdatedDec 12, 2024
• Perl

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

• UpdatedJul 27, 2025
• Python

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

• UpdatedApr 23, 2023
• Perl

Snakemake pipeline to analyze transposable element 'omics data.

• UpdatedFeb 12, 2026
• R

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

• UpdatedDec 19, 2025
• Perl

Distribution of TEs and their relationship to genes in host genome

• UpdatedJun 20, 2023
• Python

PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes

• UpdatedJan 16, 2026
• Perl

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

• UpdatedJan 26, 2026
• Python

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

• UpdatedMay 20, 2025
• Perl

Genotyping of segregating mobile elements insertions

• UpdatedJul 29, 2021
• Perl

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

• UpdatedMar 19, 2023
• C++