ontyper

Microsatellite genotyping toolkit for Oxford Nanopore sequencing data.

NOTE: This is currently in heavy development and everything is subject to change.

Installation

First you need to clone the repository:

git clone git@github.com:reslp/ontyper.git

As a global CLI tool (recommended)

# Install globally using uv tool (from local directory)
cd /path/to/ontyper
uv tool install .

# Or install directly from a git repository (once published)
# uv tool install git+https://github.com/username/ontyper.git

# The 'ontyper' command is now available globally
ontyper --help

# To upgrade later
uv tool upgrade ontyper

# To uninstall
uv tool uninstall ontyper

Usage

Demultiplex reads

ontyper demultiplex -i reads.fasta -d demultiplex.txt -o output_dir/
ontyper demultiplex -i reads.fastq.gz -d demultiplex.txt -o output_dir/

Identify genotypes

ontyper genotypes identify -d demultiplex.txt -i demultiplexed_dir/ > genotypes.tsv

# Or write the table directly to a file
ontyper genotypes identify -d demultiplex.txt -i demultiplexed_dir/ -o genotypes.tsv

# With detailed output (creates genotypes-detailed.tsv)
ontyper genotypes identify -d demultiplex.txt -i demultiplexed_dir/ --detailed -o genotypes.tsv

Extract sequences for a specific genotype

ontyper genotypes extract -i reads.fasta -g genotypes-detailed.tsv -l TTMock01_Tth445 -n 20x
ontyper genotypes extract -i reads.fastq.gz -g genotypes-detailed.tsv -l TTMock01_Tth445 -n 20x

Visualize genotype distributions

ontyper genotypes visualize -g genotypes.tsv -l TTMock01_Tth445

Build an interactive HTML report

ontyper report -d demultiplexed_dir/ -g genotypes.tsv -p allele-calls.tsv -o report.html

These features are currently in development and not yet available in the online version:

Build allele prediction features

ontyper genotypes features \
  --genotypes genotypes.tsv \
  --mapping sample_locus_mapping.csv \
  --true-alleles true_alleles.csv \
  -o training-features.csv

Omit --true-alleles to create prediction-only feature tables.

Train an allele prediction model

ontyper genotypes train \
  --features training-features.csv \
  --model HistGradientBoostingClassifier \
  --modelfile allele-model.joblib \
  --group sample_id

Predict alleles with a trained model

ontyper genotypes predict \
  --features prediction-features.csv \
  --modelfile allele-model.joblib \
  --predictions-out allele-scores.tsv \
  -o allele-calls.tsv \
  --top-k 6 \
  --prob-threshold 0.2

Run integrated model-based genotype calling

ontyper genotypes call \
  --demfile demultiplex.txt \
  --indir demultiplexed_dir/ \
  --mapping sample_locus_mapping.csv \
  --modelfile allele-model.joblib \
  -o allele-calls.tsv

Development

# Using pip (editable install)
pip install -e .

# Using uv in a virtual environment
uv venv
source .venv/bin/activate  # or .venv-mba/bin/activate on some systems
uv pip install -e .

# Install with dev dependencies
pip install -e ".[dev]"

# Run tests
pytest