LTR-checker: deep-learning guided structural identification of LTR retrotransposon providing decreased computation demand and high flexibility
- Install
conda create -n ltr_checker python=3.8
conda activate ltr_checker
pip3 install -r requirements.txt
conda install ltr_finder -c bioconda
- Workflow
- Usage
python3 ltr_finder.py --genome <genome_file> --threads <num_threads> --output <output_path> --stride <stride_value> --max <max_distance> --min <min_distance> --max_ltr <max_ltr_length> --min_ltr <min_ltr_length> --tgca <tgca_option> --tsd <tsd_option> --model <model_path> --split <num_segments>
- Options
· --genome: Path to the input genome file (required).
· --threads: Number of threads to use (default=10).
· --output: Path to the output directory (required).
· --stride: Stride value for processing (default=10000).
· --max: Maximum separation distance of two LTR elements (default=15000).
· --min: Minimum separation distance of two LTR elements (default=1000).
· --max_ltr: Maximum length of LTR elements (default=7000).
· --min_ltr: Minimum length of LTR elements (default=100).
· --tgca: Specify whether TGCA is needed (default=no).
· --tsd: Specify whether TSD is needed (default=no).
· --model: Path to the machine learning model file (required).
· --split: Number of chromosome segmentation (default=100).