The details of the scripts to detect non-reference transposable element insertions from short-read sequencing data is described in Baduel et al. MMB 2021 10.1007/978-1-0716-1134-0_15.
accessory scripts and file for A. thaliana: /thaliana
Accessory files and wrapper scripts are available in /thaliana to run the SPLITREADER pipeline on the A. thaliana genome.
In addition to the TE annotation files provided a fasta file of the reference genome need to be downloaded from arabidopsis.org (e.g. tair10)
The main wrapper script /thaliana/Submit_thaliana_SPLITREADER.sh can then be used to run all the steps of the pipeline.
If you have any question please contact me through the channels listed here.