其他工具

https://github.com/dparks1134/RefineM

refineM

安装

sudo apt install python-pip
pip install matplotlib==2.2.3 -i https://pypi.tuna.tsinghua.edu.cn/simple
sudo pip install refinem -i https://pypi.mirrors.ustc.edu.cn/simple/
pip install pysam -i https://pypi.mirrors.ustc.edu.cn/simple/
pip install dendropy -i https://pypi.mirrors.ustc.edu.cn/simple/
sudo apt-get install python-scipy
pip install scipy -i https://pypi.mirrors.ustc.edu.cn/simple/

运行

refinem

sudo apt install python-numpy

git clone https://github.com/hyattpd/Prodigal.git
cd Prodigal/
make install

apt install ncbi-blast+

wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
cp diamond /usr/local/bin/

git clone https://github.com/marbl/Krona.git
cd Krona/KronaTools/
cd /home/llt/database/krona
./install.pl
mkdir taxonomy
sudo ./install.pl --taxonomy /home/llt/database/krona/taxonomy
sudo apt install curl
./updateTaxonomy.sh
./updateAccessions.sh

sudo apt install python-pip
sudo pip install refinem
sudo pip install pysam dendropy -i https://pypi.mirrors.ustc.edu.cn/simple/
sudo apt install python-scipy
sudo pip install matplotlib==1.5.3

checkM

安装

apt install hmmer
apt install prodigal
wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha17/pplacer-Linux-v1.1.alpha17.zip
unzip pplacer-Linux-v1.1.alpha17.zip
cd pplacer-Linux-v1.1.alpha17/
cp guppy pplacer rppr /usr/local/bin/
sudo pip install numpy checkm-genome
checkm
/mnt/d/linux/database/checkm
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar zxvf checkm_data_2015_01_16.tar.gz
checkm data setRoot