Bowtie下载安装

$ wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip/download
$ unzip bowtie2-2.2.9-linux-x86_64.zip
$ cd bowtie2-2.2.9
$ make
$ ./bowtie

Bowtie的简单比对

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# 建立索引 red_bowtie 为索引前缀
$ bowtie2-build ref.fa output_dir/ref_bowtie
# 单末端测序结果序列比对
$ bowtie2 ref_bowtie read.fastq -S result.sam
# 双末端测序结果序列比对
$ bowtie2 -x ref_bowtie -1 read1.fastq -2 read2.fastq -S result.sam

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