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  • nanopolish 安装使用

    https://github.com/jts/nanopolish

     nanopolish

    Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more

    Dependencies

    A compiler that supports C++11 is needed to build nanopolish. Development of the code is performed using gcc-4.8.

    By default, nanopolish will download and compile all of its required dependencies. Some users however may want to use system-wide versions of the libraries. To turn off the automatic installation of dependencies set HDF5=noinstallEIGEN=noinstallHTS=noinstall or MINIMAP2=noinstall parameters when running make as appropriate. The current versions and compile options for the dependencies are:

    In order to use the additional python3 scripts within /scripts, install the dependencies via

    pip install -r scripts/requirements.txt --user

    more requirements.txt
    setuptools>=42.0.2
    cython>=0.29.14
    numpy>=1.18.0
    scikit-learn>=0.22
    h5py>=2.10.0
    tqdm>=4.41.0
    matplotlib>=3.0.3
    seaborn>=0.9.0
    biopython>=1.76
    pysam>=0.15.3
    pandas>=0.24.0
    scipy>=1.3.0

     WARNING: The scripts cygdb, cython and cythonize are installed in '/root/.local/bin' which is not on PATH.

    Installation instructions

    Installing the latest code from github (recommended)

    You can download and compile the latest code from github as follows:

    git clone --recursive https://github.com/jts/nanopolish.git
    cd nanopolish
    make

     /home/software/nanopolish/nanopolish/nanopolish
     
    usage: nanopolish [command] [options]
      valid commands:
        --help
        --version
        call-methylation
        eventalign
        extract
        getmodel
        help
        index
        methyltrain
        phase-reads
        polya
        scorereads
        variants
        vcf2fasta
      for help on given command, type nanopolish command --help

    The main subprograms of nanopolish are:

    nanopolish call-methylation: predict genomic bases that may be methylated
    nanopolish variants: detect SNPs and indels with respect to a reference genome
    nanopolish variants --consensus: calculate an improved consensus sequence for a draft genome assembly
    nanopolish eventalign: align signal-level events to k-mers of a reference genome
    
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  • 原文地址:https://www.cnblogs.com/emanlee/p/13583576.html
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