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nanopolish 安装使用

时间:2023-11-02 13:06:41浏览次数:42  
标签:nanopolish -- github dependencies genome 使用 noinstall 安装

 

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



标签:nanopolish,--,github,dependencies,genome,使用,noinstall,安装
From: https://blog.51cto.com/emanlee/8143865

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