# 建立線粒體基因組序列索引
bwa index mitochondria.fasta
#mitochondria.fasta替換成已經(jīng)組裝好的線粒體基因組序列文件
# 比對
bwa mem mitochondria.fasta read1.fastq read2.fastq > alignment.sam
#sam轉(zhuǎn)bam格式
samtools view -Sb alignment.sam > alignment.bam
#bam文件排序
samtools sort alignment.bam -o sorted_alignment.bam
#samtools計算depth
samtools depth sorted_alignment.bam > depth.txt