👩‍💻

- Code -

If you have any question or comment please reach me through the channels listed there.

SPLITREADER

This public repository contains the scripts for running the SPLITREADER pipeline initially developped by Quadrana et al. eLife 2016, further improved by Baduel et al. MMB 2021, and implemented in Baduel et al. Genome Biol 2021

SPLITREADER_v1.0

This folder contains the scripts to detect non-reference transposable element insertions from short-read sequencing data as described in Baduel et al. MMB 2021.
Accessory files and wrapper scripts are also available in /thaliana to run the SPLITREADER pipeline on the A. thaliana genome.

SPLITREADER_v1.2

This folder contains a snakemake version of the SPLITREADER pipeline produced by @aurelpetit for easier portability and management of dependencies.

For citation

Baduel P, Quadrana L, Colot V. Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data. Plant Transposable Elements, Methods in Molecular Biology, 10.1007/978-1-0716-1134-0_15, 04/2021.

Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen R, Jeddeloh JA, Colot V. The Arabidopsis thaliana mobilome and its impact at the species level. eLife, 10.1007/978-1-0716-1134-0_15, 06/2016.