各软件对硬件需求是大内存,多线程。
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关于conda的说明,请参考conda
conda config –add channels defaults conda config –add channels bioconda conda config –add channels conda-forge
conda install -c bioconda canu
conda install -c bioconda/label/cf201901 canu
conda create -n python2 python=2.7
conda activate python2
pip install psutil
mkdir -p ~/opt/biosoft/
cd ~/opt/biosoft/``
wget https://github.com/Nextomics/NextDenovo/releases/download/v2.0-beta.1/NextDenovo.tgz
tar -zxvf NextDenovo.tgz
~/opt/biosoft/NextDenovo/nextDenovo -h
conda install -c conda-forge falcon
conda install -c conda-forge/label/gcc7 falcon
conda install -c conda-forge/label/cf201901 falcon
conda install -c conda-forge/label/cf202003 falcon
conda install -c bioconda wtdbg
conda install -c bioconda/label/cf201901 wtdbg
内存需求和测序数据量和基因组大小有关,内存>=1T, CPU>100核,单次运行时间7天左右(取决于硬件和基因组大小)。
下游分析用到的软件比较烦杂,很多不能直接用conda安装,主要有:
conda install -c bioconda -c conda-forge busco=4.0.6
conda activate base
conda install -c bioconda repeatmodeler
conda install -c bioconda/label/cf201901 repeatmodeler
conda install -c bioconda maker
conda install -c bioconda/label/cf201901 maker
conda install -c bioconda braker
conda install -c bioconda/label/cf201901 braker
conda install -c bioconda augustus
conda install -c bioconda/label/cf201901 augustus