geNomad，DeepMicroClass，DeepVirFinder，VirSorter2，VIBRANT，PPR-Meta安装与使用

geNomad安装

GitHub - apcamargo/genomad: geNomad: Identification of mobile genetic elements

mamba create -n genomad -c conda-forge -c bioconda genomad=1.7.4
mamba activate genomad
genomad download-database {dir}
genomad end-to-end -h

DeepMicroClass安装

GitHub - chengsly/DeepMicroClass

pip install DeepMicroClass
DeepMicroClass predict -h

DeepVirFinder安装

GitHub - jessieren/DeepVirFinder: Identifying viruses from metagenomic data by deep learning

conda create --name dvf python=3.6 numpy theano=1.0.3 keras=2.2.4 scikit-learn Biopython h5py
source activate dvf
git clone https://github.com/jessieren/DeepVirFinder
cd DeepVirFinder
chmod 755 *.py
~/DeepVirFinder/dvf.py -h

VirSorter2安装

GitHub - jiarong/VirSorter2: customizable pipeline to identify viral sequences from (meta)genomic data

mamba create -n vs2 -c conda-forge -c bioconda "python>=3.6,<=3.10" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer==3.3 prodigal screed ruamel.yaml "snakemake>=5.18,<=5.26" click "conda-package-handling<=1.9"
mamba activate vs2
mkdir VirSorter2
cd VirSorter2
git clone https://github.com/jiarong/VirSorter2.git
cd VirSorter2
pip install -e .
#下载数据库
https://osf.io/v46sc/download
tar -xzf db.tgz
virsorter config --init-source --db-dir=./db

VIBRANT安装

GitHub - AnantharamanLab/VIBRANT: Virus Identification By iteRative ANnoTation

conda create -n vibrant python=3 pandas numpy scikit-learn=0.21.3 prodigal hmmer biopython matplotlib seaborn
conda install -c bioconda vibrant==1.2.1
download-db.sh {dir}
~/mambaforge/envs/vibrant/bin/VIBRANT_run.py

 PPR-Meta安装

GitHub - zhenchengfang/PPR-Meta: A tool for identifying phages and plasmids from metagenomic fragments using deep learning

cd PPR-meta
docker pull shufangwu/ppr-meta:1.0
docker images
docker run -it shufangwu/ppr-meta:1.0 bash
cd /home/PPR-Meta
./PPR_Meta example.fna result.csv
exit
如果你只想退出并保持容器运行，你可以按Ctrl+P+Q
#共享文件夹
docker run -it -v {宿主机}:/home/PPR-Meta shufangwu/ppr-meta:1.0 bash