HLA typing

Introduction

mhcflow is an end-to-end workflow designed to accurately genotype MHC class I and II alleles. It streamlines the process of generating analysis-ready outputs that support both HLA loss of heterozygosity (LOH) detection and peptide binding prediction.

Features

mhcflow builds upon the well-established Polysolver algorithm, adding modern enhancements and additional functionality:

• Supports both class I and II typing

  mhcflow expands on original approach by supporting both class I and class II typing while maintaining high accuracy.

• Modern, modular design

  • Re-engineered with a modular architecture for better flexibility and maintainability

  • Streamlined workflows that minimize I/O operations

  • Optimized runtime, ensuring faster analysis without compromising quality

  • Minimal hard-coded logic, facilitating easier customization and integration

• User-friendly integration

  Easily incorporate mhcflow into modern whole-genome, whole-exome pipelines through its command line interface.

• Analysis-ready

  Generates results can be directly used for HLA LOH detection and peptide binding prediction.

Installation

Starting from v0.2.0, mhcflow can be installed from PyPI:

pip install mhcflow

If you prefer to use the shell script implementation, please refer to the instruction on the Installation page.

Citation

Please cite the original Polysolver paper.

If you use mhcflow, please cite this github repo as well.