Please move to mMHtyper[https://github.com/willow2333/mMHtyper], which is the update version of the MHtyper!
MHtyper is an end-to-end pipeline for recognizing the Forensic microhaplotypes in Nanopore sequencing data. It is implemented using Python.
Sequencing data was filtered by NanoFilt and aligment with minimap2
Files with both BED and pileup format are generated
Phasing with margin ; Correction with isONcorrect; Haplotype analysis by MHtyper ; Integrate the analysis results to get the final micro haplotype results
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: 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
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
The snp-sites.txt that contained the information of samples must needed
The analysis results of microhaplotypes is in finalphase.txt
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 (forensic@scu.edu.cn), Zheng Wang (wangzhengtim@scu.edu.cn), Liu Qin (ql_willow@163.com)