建议新建biosoft、bin、src文件夹分别放置源文件、快捷方式、安装压缩包

一、序列比对

1 blast+

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz
tar -zxvf ncbi-blast-2.12.0+-x64-linux.tar.gz
cd ~/biosoft/ncbi-blast-2.10.1+/bin
ls -1  | while read i;do ln -s $PWD/$i ~/bin/;done;

2 diamond #类似于blast，其速度巨快

http://www.diamondsearch.org/index.php  #网址
wget http://github.com/bbuchfink/diamond/releases/download/v0.9.36/diamond-linux64.tar.gz
tar -zxvf diamond-linux64.tar.gz  

3 bowtie2 #测序序列与参考序列比对

依赖python运行
bowtie2-build、bowtie2常用

wget https://jaist.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip
unzip bowtie2-2.3.5.1-linux-x86_64.zip 
ln -s ~/biosoft/bowtie2-2.3.5.1-linux-x86_64/bowtie2-build ~/bin
ln -s ~/biosoft/bowtie2-2.3.5.1-linux-x86_64/bowtie2 ~/bin

二、NCBI及转录组

4 edirect #NCBI下载数据用命令行下载

efetch和edirect py常用

wget  https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz
tar -zxvf edirect.tar.gz 
cd ~/bin/
./vdb-config --interactive  
ln -s ~/biosoft/edirect/efetch .
ln -s ~/biosoft/edirect/edirect.pl .

5 sratookit #批量下载NCBI SRA数据库中的测序数据

区分CentOS和Ubuntu版本
prefetch、fasterq-dump、fastq-dump

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.11.3/sratoolkit.2.11.3-centos_linux64.tar.gz
tar -zxvf sratoolkit.2.11.3-centos_linux64.tar.gz
./vdb-config --interactive  #下载数据可远程连接
ln -s  ~/biosoft/sratoolkit.2.11.1-centos_linux64/bin/prefetch ./
ln -s  ~/biosoft/sratoolkit.2.11.1-centos_linux64/bin/fasterq-dump ./
ln -s  ~/biosoft/sratoolkit.2.11.1-centos_linux64/bin/fastq-dump ./

6 aspera #快速下载数据

wget https://download.asperasoft.com/download/sw/connect/3.9.9/ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz
tar -zxvf ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz
sh ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh  #运行

7 fastqc #RNA-Seq测序数据质控

安装后fastqc显示无权限执行，更改权限设置755
有图形化窗口，可以用xmanger打开

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
unzip fastqc_v0.11.9.zip 
chmod 755  ~/biosoft/FastQC/fastqc 
ln -s ~/biosoft/FastQC/fastqc ~/bin

8 fastp #过滤数据

电脑端下载后通过xftp传输到biosoft文件夹内https://github.com/OpenGene/fastp#get-fastp
chmod 755 ./fastp #更改权限设置

9 hisat2 #一种高效的RNA-seq实验比对工具

https://daehwankimlab.github.io/hisat2/  #网址
wget -c https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz
tar -zxvf  grch38_genome.tar.gz
ln -s ~/biosoft/hisat2-2.2.0/hisat2-build ~/bin/
ln -s ~/biosoft/hisat2-2.2.0/hisat2 ~/bin/

10 stringtie #转录组组装及定量

http://ccb.jhu.edu/software/stringtie/index.shtml  #网址
wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.1.3b.Linux_x86_64.tar.gz
tar -zxvf stringtie-2.1.3b.Linux_x86_64.tar.gz/
ln -s ~/biosoft/stringtie-2.1.3b.Linux_x86_64/stringtie ~/bin/

11 spades #二代测序基因组拼接软件

spades.py是一个脚本程序，将单个功能串联起来了

wget http://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1-Linux.tar.gz
tar -zxvf SPAdes-3.14.1-Linux.tar.gz
ln -s ~/biosoft/SPAdes-3.14.1-Linux/bin/spades.py ~/bin
python spades.py  #打开