Linux command
bowtie2 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Align reads
bowtie2 -x [genome_index] -1 [reads_1.fq] -2 [reads_2.fq] -S [output.sam]
Align single-end reads
bowtie2 -x [genome_index] -U [reads.fq] -S [output.sam]
Use multiple threads
bowtie2 -p [8] -x [genome_index] -1 [reads_1.fq] -2 [reads_2.fq] -S [output.sam]
Build an index
bowtie2-build [reference.fa] [index_base]
Align with local
bowtie2 --local -x [genome_index] -U [reads.fq] -S [output.sam]
Very sensitive alignment
bowtie2 --very-sensitive -x [genome_index] -1 [r1.fq] -2 [r2.fq] -S [out.sam]
Output unaligned reads
bowtie2 -x [genome_index] -U [reads.fq] -S [output.sam] --un [unaligned.fq]
说明
bowtie2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 to 1000 base pairs to relatively large genomes like the human genome. Bowtie2 uses an FM Index (based on the Burrows-Wheeler transform) for the reference genome, enabling fast alignment while maintaining low memory usage. It supports gapped, local, and paired-end alignment modes. The alignment output is SAM format, which can be processed by samtools and other downstream tools for variant calling, expression analysis, and other genomics workflows.
参数
- -x _index_
- Index filename prefix (built with bowtie2-build).
- -1 _reads_
- Comma-separated files with #1 mates.
- -2 _reads_
- Comma-separated files with #2 mates.
- -U _reads_
- Comma-separated files with unpaired reads.
- -S _sam_
- Output SAM file.
- -p _threads_
- Number of parallel threads.
- --local
- Local alignment mode (soft-clipping).
- --end-to-end
- End-to-end alignment (default).
- --very-fast
- Preset for very fast alignment.
- --sensitive
- Preset for sensitive alignment (default).
- --very-sensitive
- Preset for very sensitive alignment.
- --un _file_
- Write unaligned reads to file.
- --al _file_
- Write aligned reads to file.
- -q
- Input files are FASTQ (default).
- -f
- Input files are FASTA.
FAQ
What is the bowtie2 command used for?
bowtie2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 to 1000 base pairs to relatively large genomes like the human genome. Bowtie2 uses an FM Index (based on the Burrows-Wheeler transform) for the reference genome, enabling fast alignment while maintaining low memory usage. It supports gapped, local, and paired-end alignment modes. The alignment output is SAM format, which can be processed by samtools and other downstream tools for variant calling, expression analysis, and other genomics workflows.
How do I run a basic bowtie2 example?
Run `bowtie2 -x [genome_index] -1 [reads_1.fq] -2 [reads_2.fq] -S [output.sam]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -x _index_ do in bowtie2?
Index filename prefix (built with bowtie2-build).