MHC-annotation

Tools to annotate haplotypes of MHC with gene and transcript information

Dependencies

There is only a few dependencies which you have to take care of yourself.

conda environment

The easiest way to take of these dependencies is to utilize the environment.yml in this repository to create a conda environment. conda create --name mhca -f environment_mhca.yml

manually

The script assumes that you have minimap2 installed and that it is callable with minimap2 on the command line. There are several ways to install this dependency depending on your environment. Giving two examples:

• sudo apt-get install minimap2
• conda install -c bioconda minimap2

You will also need the python packages biopython and bcbio-gff. You can install them in a conda environment with:

• conda install -c bioconda bcbio-gff
• conda install -c bioconda biopython

Install

Install this package with pip.

pip install MHC-annotation

Usage

This tools assumes that you are trying to annotate a sequence that stems from the human MHC region (also known as: HLA-region). If you supply any other sequence, you will most likely receive no meaningful result. You can annotate a fasta file with the following command:

mhca annotate <your_sequence.fa> <output_folder>

You can check whether the transcript in the resulting gff file would produce meaningful products.

mhca check_CDS <your_sequence.fa> <output_folder/your_sequence.gff>