生信软件下载网站

1.序列比对软件

局部比对软件(MUSCLE,MUMMER,Clustalw)
#下载muscle
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar -xzf muscle3.8.31_i86linux64.tar.gz 
在线网页版:https://www.ebi.ac.uk/Tools/msa/muscle/

全局比对软件(BLAST,BLAT, Blastz ...)


短序列比对(BWA,Bowtie2,SOAPalign)
下载SOAP2
wget http://soap.genomics.org.cn/down/soap2.21release.tar.gz
tar -xzf soap2.21release.tar.gz

2.处理GTF/GFF文件

gffread:[Programs for processing GTF/GFF files] 处理GTF/GFF的programs

gffread官网： http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread_ex
安装gffread:
#1
wget http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.12.Linux_x86_64.tar.gz
tar -xzf gffread-0.9.12.Linux_x86_64.tar.gz
#2
cd /some/build/dir
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
cd gffread
make

3.kmer计数软件

安装jellyfish
$ wget http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.10.tar.gz
$ tar zxvf jellyfish-1.1.10.tar.gz
$ mkdir jellyfish
$ cd jellyfish-1.1.10
$ ./configure --prefix=$PWD/../jellyfish
如果安装在当前目录中，会报错。
$ make -j 8
$ make install

4.bwa,samtools,bcftools安装

#安装samtools
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar jxvf samtools-1.9.tar.bz2
./configure --prefix=/where/to/install
make
make install

#安装bwa
wget https://nchc.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar jxvf bwa-0.7.17.tar.bz2
make

#安装bcftools
wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
tar jxvf bcftools-1.9.tar.bz2
./configure
make 
make install

#安bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
tar zxvf bedtools-2.27.1.tar.gz
make
cp/bin/* usr/local/bin/

#安装bamdst
git clone https://github.com/shiquan/bamdst
make

#安装vcftools
git clone https://github.com/vcftools/vcftools.git
cd vcftools/ 
./autogen.sh 
./configure 
make 
make install

6.SOAPdenovo

wget https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/bin/r240/SOAPdenovo2-bin-LINUX-generic-r240.tgz
tar -zxf SOAPdenovo2-src-r240.tgz