BSA分析-实战笔记(一)软件安装

参考：
以水稻为例教你如何使用BSA方法进行遗传定位（上篇） - (jianshu.com)

1. seqkit：序列处理软件

conda install seqkit

2. fastp：数据质控

conda install fastp

3. bwa：数据比对到参考基因组

conda install bwa

4. samtools：处理sam/bam文件

mkdir samtools
cd samtools
wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
tar xvf samtools-1.15.1.tar.bz2
cd samtools-1.15.1.tar.bz2/
./configure --prefix=/data/kesimin/softwares/samtools/samtools-1.15.1
make
make install
##添加环境变量
echo 'PATH=/data/xxx/softwares/samtools/samtools-1.15.1/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

5. sambamba：标记重复序列

mkdir sambamba
cd sambamba
wget https://github.com/biod/sambamba/releases/download/v0.8.2/sambamba-0.8.2-linux-amd64-static.gz
gunzip sambamba-0.8.2-linux-amd64-static.gz
mv sambamba-0.8.2-linux-amd64-static.gz sambamba
chmod a+x sambamba
echo 'PATH=/data/xxx/softwares/sambamba/sambamba:$PATH' >> ~/.bashrc
source ~/.bashrc

6. bcftools：处理vcf/bcf，变异检测

 wget -c https://github.com/samtools/bcftools/releases/download/1.15.1/bcftools-1.15.1.tar.bz2
tar xvf bcftools-1.15.1.tar.bz2
cd bcftools-1.15.1/
./configure --prefix=/data/xxx/softwares/bcftools-1.15.1/htslib-1.15.1
make
make install
###添加进环境变量
echo 'PATH=/data/xxx/softwares/bcftools-1.15.1/htslib-1.15.1/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

7. R：数据分析