Bowtie 2是一种超快速且高效存储的工具，可用于将测序序列与参考序列进行比对。
https://github.com/BenLangmead/bowtie2
建立参考基因组索引 # Building a small indexbowtie2-build example/reference/lambda_virus.fa example/index/lambda_virus# Building a large indexbowtie2-build --large-index example/reference/lambda_virus.fa example/index/lambda_virus 测序文件（fastq）与参考基因对比（mapping） # Aligning unpaired readsbowtie2 -x example/index/lambda_virus -U example/reads/longreads.fq -S out.sam# Aligning paired readsbowtie2 -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq -S out.sam fastq fasta格式转化fastq fasta格式转化
sam bam转化 (samtools工具) # BAM -> SAMsamtools view -h -o out.sam out.bam# SAM -> BAMsamtools view -bS out.sam >out.bam#-b 输出BAM format#-S 输入SAM格式