Linux command
minimap2 命令
文本
涉及管道、覆盖或删除，执行前请先确认路径和参数。
常用示例
Map long reads to reference
minimap2 -a [reference.fa] [reads.fq] > [aligned.sam]
Map with preset for ONT reads
minimap2 -ax map-ont [reference.fa] [ont_reads.fq] > [aligned.sam]
Map PacBio HiFi reads
minimap2 -ax map-hifi [reference.fa] [hifi.fq] > [aligned.sam]
Map short reads
minimap2 -ax sr [reference.fa] [reads_1.fq] [reads_2.fq] > [aligned.sam]
Create index
minimap2 -d [reference.mmi] [reference.fa]
Use multiple threads
minimap2 -t [8] -ax map-ont [reference.fa] [reads.fq] > [aligned.sam]
说明
minimap2 is a versatile sequence aligner for DNA and RNA sequences. It can align long reads from PacBio or Oxford Nanopore, short reads, and even whole assemblies. minimap2 is extremely fast and memory-efficient, becoming the standard for long-read alignment.
参数
- -a
- Output SAM format.
- -x _preset_
- Preset (map-ont, map-pb, map-hifi, sr, asm5).
- -t _threads_
- Number of threads.
- -d _file_
- Save index to file.
- -o _file_
- Output file.
- -k _k_
- K-mer size.
- -w _w_
- Minimizer window.
FAQ
What is the minimap2 command used for?
minimap2 is a versatile sequence aligner for DNA and RNA sequences. It can align long reads from PacBio or Oxford Nanopore, short reads, and even whole assemblies. minimap2 is extremely fast and memory-efficient, becoming the standard for long-read alignment.
How do I run a basic minimap2 example?
Run `minimap2 -a [reference.fa] [reads.fq] > [aligned.sam]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -a do in minimap2?
Output SAM format.