MHtyper is an end-to-end pipeline for recognized the Forensic microhaplotypes in Nanopore sequencing data.

   conda create -n MHtyper 
   conda activate MHtyper
   conda config --add channels bioconda 
   conda config --add channels
   conda-forge conda install -y NanoFilt minimap2 samtools bedtools

# isONcorrect installation

   git clone https://github.com/ksahlin/isONcorrect.git
   cd isONcorrect 
   ./isONcorrect

# Marin installation
# step1:
   sudo apt-get install git make gcc g++ autoconf zlib1g-dev libcurl4-openssl-dev libbz2-dev libhdf5-dev
   wget https://github.com/Kitware/CMake/releases/download/v3.14.4/cmake-3.14.4-Linux-x86_64.sh && sudo mkdir /opt/cmake &&
   sudo sh cmake-3.14.4-Linux-x86_64.sh --prefix=/opt/cmake --skip-license && sudo ln -s /opt/cmake/bin/cmake
   /usr/local/bin/cmake cmake --version

# step2: Check out the repository and submodules:

   git clone https://github.com/UCSC-nanopore-cgl/margin.git
   cd margin git submodule update --init

# step3: Make build directory:

   mkdir build cd build

# step4: Generate Makefile and run:

   cmake .. 
   make ./margin

   git clone https://github.com/willow2333/MHtyper.git
   cd MHtyper 
   python run.py --h
   
   usage: run.py [-h] [--fastqfiles FASTQFILES] [--reference REFERENCE] [--prefix PREFIX] [--truthvcf TRUTHVCF] [--marginpath MARGINPATH]

    optional arguments:
      -h, --help            show this help message and exit
      --fastqfiles FASTQFILES
                            The input *.fq.gz files.
      --reference REFERENCE
                            The path of your ref.
      --prefix PREFIX       The name of your Sample, default is "Test".
      --truthvcf TRUTHVCF   The truth variant files in your research.
      --marginpath MARGINPATH
                            The setup path of "Margin".

   cd ./Test
   python ../run.py --fastqfiles test.fq.gz --reference path/hg19.fa --prefix Test --truthvcf truthvcf.txt  --marginpath path/margin