Anvi’o 安装

Dependencies

• DIAMOND or NCBI’s blastp for search.
• MCL for clustering.
• muscle for alignment.

easy install through conda:

wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod 777 Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
#在询问是否将conda加入环境变量的时候选择no
cd miniconda3/bin/
chmod 777 activate
. ./activate
#添加频道
conda config --env --add channels conda-forge
conda config --env --add channels bioconda

conda create -n anvio-6 python=3.6
conda activate anvio-6
conda install -y anvio=6
conda install -y diamond=0.9.14

具体用法 anvi’o官网教程：http://merenlab.org/2016/11/08/pangenomics-v2/

提取单拷贝同源基因

anvi-get-sequences-for-gene-clusters -p AH_all_Pan-PAN.db -g ../PROCHLORO-GENOMES.db -o SCG.fasta --max-num-genes-from-each-genome 1 --min-num-genomes-gene-cluster-occurs 85
grep '>' SCG.fasta | wc -l
#结果除以85就是单拷贝同源基因的数量
anvi-get-sequences-for-gene-clusters -p AH_all_Pan-PAN.db -g ../PROCHLORO-GENOMES.db -o Singletons.fasta -C default -b Singletons
#提取感兴趣的bin