• Dynamont is a segmentation/resquiggling tool for ONT signals.

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

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Dynamont

TODO: change title A dynamic programming algorithm to resquiggle and segment the raw ONT signal.

TODO: add readme TODO: create conda package of tool TODO: build tool with subtools

Installation

Pypi/pip

pip install dynamont

Conda

conda install mamba
mamba create -n dynamont -c jannessp dynamont
conda activate dynamont

Usage

TODO

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: dynamont-NTK specific: alignment score (Z) does not match between forward and backward run in preprocessing on signal (T) and read (N) in function: preProcTN
• 2: dynamont-NTK specific: alignment score (Z) does not match between forward and backward run in preprocessing on signal (T) and de novo calling (K) in function: preProcTK
• 3: Alignment score (Z) does not match between forward and backward run in main function 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
• 6: Model file contains a k-mer that does not match the k-mer size of the pore
• 7: Invalid model path was provided
• 8: Provided ONT signal too short
• 9: Provided reads too short
• 10: Signal is smaller than read
• 11: Read is smaller than kmerSize of pore type