For more detailed descriptions see pbaduel.com/code.
If you have any question or comment please reach me through the channels listed there.
SPLITREADER pipeline and accessory scripts and file for A. thaliana: /SPLITREADER
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 available in /thaliana to run the SPLITREADER pipeline on the A. thaliana genome.
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.