Telogator2

A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads.

If this software has been useful for your work, please cite us at:

Stephens, Z., & Kocher, J. P. (2024). Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC bioinformatics, 25(1), 194.

https://link.springer.com/article/10.1186/s12859-024-05807-5

Installation (conda env):

Telogator2 dependencies can be easily installed via conda:

git clone https://github.com/zstephens/telogator2.git && cd telogator2/

# create & activate conda environment
conda env create -f conda_env_telogator2.yaml
conda activate telogator2

# run test data
python telogator2.py -i test_data/hg002-ont-1p.fa.gz \ 
                     -o results/ \ 
                     -r ont

Installation (pip):

python3.12 -m venv venv
source activate venv/bin/activate
pip install git+https://github.com/zstephens/telogator2.git@v2.2.2

# run test data
telogator2 -i test_data/hg002-ont-1p.fa.gz \ 
           -o results/ \ 
           -r ont \ 
           --minimap2 /path/to/minimap2

Notes:

An…