clemgoub

dnaPipeTE

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).

TE-Aid

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

TypeTE

Genotyping of segregating mobile elements insertions

rm2gff3

Convert RepeatMasker ".out" file into a gff3 with colors!!!

dnaPT_utils

A collection of scripts to perform several downstream analyses with dnaPipeTE 1.3

consensus2genome

[DEPRECATED] R function that blast any TE consensus to reference genome and output mapping graph

So2

So2 TE Bioinformatic ressources -- Parisot et al. 2020

dnaPipeTE2

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

typeref

Bi-allelic genotyping of reference transposable elements

denovoTE-eval

Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"

FraHMMER

Frameshift Aware Translated Alignments

LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts

pMEsim

polymorphic mobile element simulator

REPCLASS

This tool facilitates transposable elements consensus classification

RPi_GPIO_basics

Basics GPIO projects for Raspberry Pi

TD_albo

Suite of scripts used for the production of Transposable Elements polymorphism (High-Throughput Transposon Display) data in 140 individuals of Aedes albopictus. Used in Goubert et al. bioRxiv: https://doi.org/10.1101/049197