A Dynamic Programming Approach to Segment ONT Signals. Dynamont is a segmentation/resquiggling tool for ONT signals. Dynamont was tested on * RNA002 * RNA004 * DNA R10.4.1 5kHz (I applied the trained transition parameters from the RNA004 model to the DNA R10 models. These should be fine-tuned for the DNA models.)

• Installation
  • Pypi/pip
  • Conda
• Usage
• Default models:
• Output
  • Example Output
• Exit-Codes

Installation

Pypi/pip

bash pip install dynamont

Conda

bash conda config --add channels jannessp # to install all dependencies from the correct channel conda create -n dynamont jannessp::dynamont conda activate dynamont

Usage

```bash

segment a dataset

dynamont-resquiggle -r -b --mode basic -o -p

train model

dynamont-train -r -b --mode basic -o

-p

choosing a pore will automatically load the default model for that pore, a custom model can be used with the parameter --pore_model

```

Default models:

• rna_r9 (tested)
• rna_rp4 (tested)
• dna_r9 not available yet
• dna_r10.4.1 260 bps (not tested)
• dna_r10.4.1 400 bps (tested)

Output

Dynamont produces a tabular output with the following columns:

| Column Name | Description | |-------------------------|-------------| | readid | Unique identifier for the read. | | signalid | Identifier for the signal corresponding to the read. | | start | Start position of the signal segment in the read. | | end | End position of the signal segment in the read. | | basepos | Reference base position in the genomic sequence. | | base | The detected base at this position. | | motif | The surrounding sequence motif in which the base appears. | | state | The methylation state (or modification state) of the base. | | posterior_probability | Probability assigned to the predicted segment. | | polish | Polished kmer, only available in resquiggle mode. |

Example Output

Below is an example of the output generated by Dynamont:

csv readid,signalid,start,end,basepos,base,motif,state,posterior_probability,polish 476b4ed2-7865-4f81-9f78-82d614fb40a2,476b4ed2-7865-4f81-9f78-82d614fb40a2,12762,12777,53,A,AAAAAAAAA,M,0.12434,NA 476b4ed2-7865-4f81-9f78-82d614fb40a2,476b4ed2-7865-4f81-9f78-82d614fb40a2,12777,12791,52,A,AAAAAAAAA,M,0.12146,NA 476b4ed2-7865-4f81-9f78-82d614fb40a2,476b4ed2-7865-4f81-9f78-82d614fb40a2,12791,12806,51,A,AAAAAAAAA,M,0.11881,NA 476b4ed2-7865-4f81-9f78-82d614fb40a2,476b4ed2-7865-4f81-9f78-82d614fb40a2,12806,12820,50,A,AAAAAAAAA,M,0.11665,NA

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
• 6: raw file does not exist
• 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
• 20: Terminated using KeyboardInterrupt (Ctrl + C)