Linux command
bwa 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Index
bwa index [path/to/reference.fa]
Example
bwa mem -t 32 [path/to/reference.fa] [path/to/read.fq.gz] | gzip > [path/to/alignment.sam.gz]
Example
bwa mem -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]
Example
bwa mem -M -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]
Example
bwa mem -C -t 32 [path/to/reference.fa] [path/to/read_1.fq.gz] [path/to/read_2.fq.gz] | gzip > [path/to/alignment.sam.gz]
说明
bwa (Burrows-Wheeler Aligner) is a software package for mapping low-divergent DNA sequences against a large reference genome, such as the human genome. It uses the Burrows-Wheeler Transform to build an index of the reference. The mem algorithm is recommended for most applications, supporting reads from 70bp to a few megabases and providing accurate mapping.
参数
- -t _threads_
- Number of CPU threads
- -M
- Mark shorter splits as secondary (Picard compatible)
- -C
- Append FASTA/Q comment to output
- -R _string_
- Read group header line
- -o _file_
- Output file name
FAQ
What is the bwa command used for?
bwa (Burrows-Wheeler Aligner) is a software package for mapping low-divergent DNA sequences against a large reference genome, such as the human genome. It uses the Burrows-Wheeler Transform to build an index of the reference. The mem algorithm is recommended for most applications, supporting reads from 70bp to a few megabases and providing accurate mapping.
How do I run a basic bwa example?
Run `bwa index [path/to/reference.fa]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -t _threads_ do in bwa?
Number of CPU threads