tSplit the TE-splitter

Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Returns compontent segments of the element for use with transposon mapping tools.

Optionally, tsplit TIR can also compose synthetic MITES from complete DNA transposons.

Installing tSplit

Requirements:

• pymummer version >= 0.10.3 (with wrapper for nucmer option --diagfactor.)
• MUMmer4
• BLAST+ (Optional)

You can create a Conda environment with these dependencies using the YAML file in this repo.

conda env create -f environment.yml

conda activate tsplit

After activating the tsplit environment you can use pip to install the latest version of tsplit.

Installation options:

1. Install from PyPi. This will get you the latest stable release.

pip install tsplit

1. Pip install directly from this git repository.

This is the best way to ensure you have the latest development version.

pip install git+https://github.com/Adamtaranto/tSplit.git

Algorithm overview

tSplit attempts to identify terminal repeats in transposable elements by first aligning each element to itself using blastn or nucmer, and then applying a set of tuneable heuristics to select an alignment pair most likely to represent an LTR or TIR, as follows:

1. Exclude all diagonal/self-matches
2. If tsplit LTR: Retain only alignment pairs on the same strand (tandem repeats)
3. If tsplit TIR: Retain only alignment pairs on opposite strands (inverse repeats)
4. Retain pairs for which the 5' match begins within x bases of element start and whose 3' match ends within x bases of element end
5. If multiple candidates remain select alignment pair with largest internal segment (i.e. closest to element ends)