A Dynamic Programming Approach to Segment ONT Signals. Dynamont is a segmentation/resquiggling tool for ONT signals.

---

• Installation
  • Pypi/pip
  • Conda
• Usage
• Exit-Codes

---

Installation

Pypi/pip

pip install dynamont

Conda

conda create -n dynamont jannessp::dynamont
conda activate dynamont

Usage

# segment a dataset
dynamont-resquiggle -r <path/to/pod5/dataset/> -b <basecalls.bam> --mode basic --model_path <path/to/model> -o <output.csv> -p <pore>

# train model
dynamont-train -r <path/to/pod5/dataset/> -b <basecalls.bam> --mode basic --model_path <path/to/init/model> -o <output/path> -p <pore>

Exit-Codes

• -11: Segmentation fault
• -9: Out of Memory error. Decrease the number of processes or move to a system with more memory.
• -6: std::bad_alloc
• 1: resquiggle mode specific: alignment score (Z) does not match between forward and backward run in preprocessing on signal (T) and read (N).
• 2: resquiggle mode specific: alignment score (Z) does not match between forward and backward run in preprocessing on signal (T) and error correction (C).
• 3: Alignment score (Z) does not match between forward and backward pass or is -Infinity
• 4: Input signal is missing or not found in stdin stream
• 5: Input read is missing or not found in stdin stream
• 7: Invalid model path was provided
• 8: Provided ONT signal is too short
• 9: Read is too short
• 10: Signal is smaller than read
• 11: Read is smaller than kmerSize of provided pore model