Overview

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

MHtyper workflow

Step1：

 Sequencing data was filtered by NanoFilt and aligment with minimap2

Step2：

 Files with both BED and pileup format are generated

Step3：

 Phasing with margin ; Correction with isONcorrect; Haplotype analysis by MHtyper ; Integrate the analysis results to get the final micro haplotype results

Python environment construction and required software installation

   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 & Margin installation

  isONcorrect: https://github.com/ksahlin/isONcorrect [1] Margin: https://github.com/UCSC-nanopore-cgl/margin

# 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

MHtyper installation

   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".

Illustration

1.Test

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

2. The sites vcf files needed

 The snp-sites.txt that contained the information of samples must needed

3. Output

 The analysis results of microhaplotypes is in finalphase.txt

Citation

  1.Sahlin, K., Medvedev, P. Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis. Nat Commun 12, 2 (2021). https://doi.org/10.1038/s41467-020-20340-8 Link.

Email: Yiping Hou ([email protected]), Zheng Wang (), Liu Qin ([email protected])

GitHub

View Github