Uncertainty aware haplotype quantification using a Bayesian model that is based on collecting evidences from Varlociraptor.
Orthanq is under active development.
Orthanq is available as a Bioconda package and can be installed via:
mamba install orthanq
Instructions to perform HLA typing is documented here: https://orthanq.github.io/docs/usage.html#hla-quantification
Instructions to perform virus lineage quantification is documented here: https://orthanq.github.io/docs/usage.html#virus-variant-quantification
The easiest way to build Orthanq is via Conda/Mamba.
First, create the environment given by the environment.yml in this repository.
mamba env create -n orthanq-dev -f environment.yml
Second, activate the environment with
mamba activate orthanq-dev
Third, conda lib location is set via
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib
Last, Orthanq can be built with:
cargo build
or
cargo build --release