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.)

Please cite 10.1093/gigascience/giag005.

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

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Segmentation Comparison

For further details please read: 10.1093/gigascience/giag005

Installation

Pypi/pip

Recommendation: use uv

uv venv path/to/venv/dynamont
source path/to/venv/dynamont/bin/activate
uv pip install dynamont

Usage

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

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

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

Default models:

• rna002 (tested)
• rna004 (tested)
• dna_r9 not available
• 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. (0-based)
end	End position of the signal segment in the read. (0-based)
basepos	Base position in the read. (0-based)
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:

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

Differences Segmentation Tools