transposons

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

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

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

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

Genotyping of segregating mobile elements insertions

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

Transposable Element Finder - Detection of active transposable elements from NGS data

Bioinformatic analysis of RNA-Seq, WGBS, and Hi-C in Arabidopsis

A Snakemake-based pipeline for processing and quality-controlling ancient and historical DNA data, including taxonomic assessment and comparative genomic analysis across time points, producing damage-rescaled, mapped reads ready for downstream analyses.

Methods for genome paper

SLURM-ready bash scripts to run the complete REPET pipeline

An R/C++ package for simulating the evolution of retrotransposons over time.

Bi-allelic genotyping of reference transposable elements

De novo repeat inference from long reads

Bioinformatics project

ShiftSCAN systematically detects chimeric and non-chimeric peptide sources by analyzing multi-frame translations in nucleotide sequences.

Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

This repository contains the code used in the Master's Thesis "Transcriptomic keys of aging" from the Master's Degree in Biomedicine and Molecular Oncology from the University of Oviedo

Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.