BWA: Burrows-Wheeler Alignment Tool比对

bwa - Burrows-Wheeler Alignment Tool

常用操作：

 建立索引：bwa index ref.fa

 单向比对：bwa mem -t 40 ref.fa reads.fq > aln-se.sam

   -t: 线程数，默认1

   -k: 最小的种子长度，默认19

   -w: 频带宽度，默认100

   -d: 默认100

   -r: 默认1.5

   -c: 默认10000

   -A: matching scores, 默认1

   -B: mismatch penalty, 默认4

   -O: gap open penalty, 默认6

   -E: gap extension penalty, 默认1

   -L: clipping penalty, 默认5

   -T: 低于分数的比对不输出，默认30

   -a: 输出所有single-end或没有比对的paird-end reads

  双向比对：bwa mem -t 40 ref.fa read1.fq read2.fq > aln-pe.sam

bwa aln ref.fa short_read.fq > aln_sa.sai

bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam

bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam

bwa bwasw ref.fa long_read.fq > aln.sam

转载于:https://www.cnblogs.com/shawn2018/p/8566016.html