基因组组装常用软件

提示

各软件对硬件需求是大内存，多线程。

关于conda的说明，请参考conda说明。

设置conda的channels

conda config –add channels defaults conda config –add channels bioconda conda config –add channels conda-forge

Canu

conda install -c bioconda canu
conda install -c bioconda/label/cf201901 canu

nextDenovo

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

或者

conda create -y -n python2 python=2.7
conda activate python2
conda install -c anaconda psutil drmaa
wget https://github.com/Nextomics/NextPolish/releases/download/v1.1.0/NextPolish.tgz
tar -vxzf NextPolish.tgz
cd NextPolish
make -j

参考：http://kazumaxneo.hatenablog.com/entry/2020/03/06/073000

Falcon

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

Wtdbg2

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：

Busco

conda install -c bioconda -c conda-forge busco=4.0.6
conda activate base

或者

conda create -n your_env_name -c bioconda -c conda-forge busco=4.0.6 python=3.x
conda activate your_env_name

RepeatModeler

conda install -c bioconda repeatmodeler
conda install -c bioconda/label/cf201901 repeatmodeler

RepeatMasker

请参考如下链接：

Maker

conda install -c bioconda maker
conda install -c bioconda/label/cf201901 maker

Braker

conda install -c bioconda braker
conda install -c bioconda/label/cf201901 braker

Augustus

conda install -c bioconda augustus
conda install -c bioconda/label/cf201901 augustus

以及这些软件的依赖。