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.
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Updated
May 10, 2024 - R
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
Transposon Insertion Finder - Detection of new TE insertions in NGS data
Genotyping of segregating mobile elements insertions
rMETL - realignment-based Mobile Element insertion detection Tool for Long read
Transposable Element Finder - Detection of active transposable elements from NGS data
Bioinformatic analysis of RNA-Seq, WGBS, and Hi-C in Arabidopsis
Library-free horizontal transfer detection, with a focus on transposable element invasions
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.
Bioinformatics project
De novo repeat inference from long reads
Bi-allelic genotyping of reference transposable elements
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"
Pipeline to detect transposable elements (TEs) insertions polymorphism
Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.
A Python3 library for transposon fingerprinting
Analysis and selection of primers for the study of transposable elements.
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