Uncertainty aware haplotype quantification using a Bayesian model that is based on collecting evidences from Varlociraptor.

Orthanq is under active development.

Installation

Orthanq is available as a Bioconda package and can be installed via:

mamba install orthanq

HLA typing

Instructions to perform HLA typing is documented here: https://orthanq.github.io/docs/usage.html#hla-quantification

Virus lineage quantification

Instructions to perform virus lineage quantification is documented here: https://orthanq.github.io/docs/usage.html#virus-variant-quantification

Building for development and manual installation

The easiest way to build Orthanq is via its pixi workspace:

pixi install
pixi run cargo build
pixi run cargo run