- apt-get安装bwa
sudo apt install bwa
已经统一安装了，不用再装了
bwa
- 下载参考基因组
mkdir ~/bwa_test -p
cd ~/bwa_test/
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/012/525/GCA_000012525.1_ASM1252v1/GCA_000012525.1_ASM1252v1_genomic.fna.gz
gunzip GCA_000012525.1_ASM1252v1_genomic.fna.gz
- 运行bwa将read比对到参考基因组
为参考基因组建立索引
bwa index GCA_000012525.1_ASM1252v1_genomic.fna -p PCC7942_index
bwa比对
bwa mem PCC7942_index /disk1/shares/Seqs/test_7942raw_1.fq.gz /disk1/shares/Seqs/test_7942raw_2.fq.gz >test_bwa_7942.sam
less test_bwa_7942.sam
- Bowtie2安装运行
mkdir bowtie2_test
cd bowtie2_test/
拷参考基因组文件
cp ../bwa_test/GCA_000012525.1_ASM1252v1_genomic.fna ./
ll
建立索引
bowtie2-build GCA_000012525.1_ASM1252v1_genomic.fna PCC7942_index
ll
bowtie2比对
bowtie2 -x PCC7942_index -1 /disk1/shares/Seqs/test_7942raw_1.fq.gz -2 /disk1/shares/Seqs/test_7942raw_2.fq.gz -S test_bowtie2.sam
ll
● 比较bwa和bowtie2运行速度
time bowtie2 -x PCC7942_index -1 /disk1/shares/Seqs/test_7942raw_1.fq.gz -2 /disk1/shares/Seqs/test_7942raw_2.fq.gz -S test_bowtie2.sam
time bwa mem -t 1 ../bwa_test/PCC7942_index /disk1/shares/Seqs/test_7942raw_1.fq.gz /disk1/shares/Seqs/test_7942raw_2.fq.gz >test_bwa_7942.sam
