Bowtie2 基因组mapping

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 index
bowtie2-build example/reference/lambda_virus.fa example/index/lambda_virus

# Building a large index
bowtie2-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 reads
bowtie2 -x example/index/lambda_virus -U example/reads/longreads.fq -S out.sam

# Aligning paired reads
bowtie2 -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 -> SAM
samtools view -h -o out.sam out.bam

# SAM -> BAM
samtools view -bS out.sam >out.bam
#-b 输出BAM format
#-S 输入SAM格式