宏基因组测序分析（一）软件安装
R 包安装
install.packages(c("pheatmap","argparser", "cowplot","ggalluvial))
install.packages(c("tidyverse", "formattable", "seqinr","pkgbuild"))
install.packages("vegan")
BiocManager::install("AnnotationForge")
BiocManager::install("clusterProfiler")
BiocManager::install("phyloseq")
BiocManager::install("PCAtools")
conda 安装
conda 主要用来创建不同环境，来安装依赖较多的软件。
从conda 官网下载最新版conda 进行安装，网址如下：https://repo.anaconda.com/archive/
# 下载
wget https://repo.anaconda.com/archive/Anaconda3-2023.03-1-Linux-x86_64.sh
# 安装
bash Anaconda3-2023.03-1-Linux-x86_64.sh
# 配置conda channels
vi ~/.condarc
channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- defaults
show_channel_urls: true
# 使用conda 安装和管理python 模块
conda install biopython
其他软件安装
比对、数据质控及fasta 序列处理
fastp
网址：https://github.com/OpenGene/fastp
# 手动安装下载即可
wget http://opengene.org/fastp/fastp
chmod a+x ./fastp
# conda 安装
conda install fastp
fastqc
网 址：https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
# 手动安装
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
unzip fastqc_v0.12.1.zip
# conda 安装
conda install fastqc
multiQC
conda install multiQC
bwa
# 手动安装
git clone https://github.com/lh3/bwa.git cd bwa
make
# conda 安装
conda install bwa
bowtie2
网址：http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
# 手动安装
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.1/bowtie2-2.5.1-linux-x86_64.zip/download
unzip bowtie2-2.5.1-linux-x86_64.zip
# conda 安装
conda install bowtie2
samtools
网址：https://github.com/samtools/samtools
# conda 安装
conda install samtools
seqtk
# 手动安装
git clone https://github.com/lh3/seqtk.git
cd seqtk
make
# conda 安装
conda install seqtk
seqkit
网址：https://bioinf.shenwei.me/seqkit/
# conda 安装
conda install seqkit
物种组成分析(这部分软件依赖比较多，建议全部使用conda安装)
kraken2、bracken、krona
# conda 安装
conda install kraken2
conda install bracken
conda install krona
lefse
网址：https://github.com/SegataLab/lefse
建议使用官网的docker容器
组装及注释及定量
megahit、
网址：https://github.com/voutcn/megahit
# 免安装，下周直接解压缩
wget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
tar -zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz
metaspades
网址：https://cab.spbu.ru/software/meta-spades/
# 免安装，下载后直接解压缩即可
wget https://cab.spbu.ru/files/release3.15.3/SPAdes-3.15.3-Linux.tar.gz
tar -zxvf SPAdes-3.15.3-Linux.tar.gz
RGI
网址：https://github.com/arpcard/rgi
# conda 安装最省事，或者使用singularity容器
conda install rgi
salmon
网址：https://github.com/COMBINE-lab/salmon
# 解压后直接使用
wget https://github.com/COMBINE-lab/salmon/releases/download/v1.6.0/salmon-1.6.0_linux_x86_64.tar.gz
tar -zxvf salmon-1.6.0_linux_x86_64.tar.gz
分箱相关
metabat2
网址：https://bitbucket.org/berkeleylab/metabat/src
# 下载解压即可
wget https://bitbucket.org/berkeleylab/metabat/downloads/metabat-static-binary-linux-x64_v2.12.1.tar.gz
tar -zxvf metabat-static-binary-linux-x64_v2.12.1.tar.gz
maxbin2
网址：http://sourceforge.net/projects/maxbin/
wget https://iweb.dl.sourceforge.net/project/maxbin/MaxBin-2.2.7.tar.gz
tar -zxvf MaxBin-2.2.7.tar.gz
cd MaxBin-2.2.7/src
make
cd ../
./autobuild_auxiliary
concoct
网址：https://concoct.readthedocs.io/en/latest/
# 使用conda安装
conda install concoct
GTDB-tk
网址：https://github.com/Ecogenomics/GTDBTk
conda create -n gtdbtk -c conda-forge -c bioconda gtdbtk
conda create -n gtdbtk-1.3.0 -c conda-forge -c bioconda gtdbtk=1.3.0
# 设置数据库路径
echo "export GTDBTK_DATA_PATH=/path/to/release/package/" > /miniconda3/envs/gtdbtk-1.3.0/etc/conda/activate.d/gtdbtk.sh
metawrap
网址：https://github.com/bxlab/metaWRAP
database 构建参考以下网址:
https://github.com/bxlab/metaWRAP/blob/master/installation/database_installation.md
