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
  1. fastp:数据质控
conda install fastp
  1. bwa:数据比对到参考基因组
conda install bwa
  1. 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:$PATH' >> ~/.bashrc
source ~/.bashrc
  1. sambamba:标记重复序列
mkdir sambamba
cd sambamba
wget https://github.com/biod/sambamba/releases/download/v0.8.2/sambamba-0.8.2-linux-amd64-static.gz
gunzip sambamba-0.8.2-linux-amd64-static.gz
mv sambamba-0.8.2-linux-amd64-static.gz sambamba
chmod a+x sambamba
echo 'PATH=/data/xxx/softwares/sambamba/sambamba:$PATH' >> ~/.bashrc
source ~/.bashrc
  1. 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
  1. R:数据分析

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