使用 Homebrew 安装 minimap2

项目链接

• 主页
• 仓库

命令和别名

• minimap2
• sdust

项目历史

Its major technical contribution is being broad without being slow. The paper describes minimap2 as usable for short reads, assembly contigs, noisy long genomic reads, RNA-seq reads, read overlap detection, and full-genome alignment. The implementation combines fast chaining with base-level alignment improvements, including Suzuki-Kasahara dynamic programming, to make long-read and splice-aware alignment practical. The project README highlights the same practical presets: PacBio and Oxford Nanopore genomic reads, Iso-Seq and Nanopore RNA/cDNA alignment, Illumina reads, assembly-to-assembly comparison, and related-species genome alignment.

使用方式

minimap2 became a core bioinformatics command-line tool because long-read sequencing workflows needed one aligner that could cover many data types. It is invoked directly in pipelines and through higher-level platforms, producing SAM or PAF output for downstream tools such as samtools, variant callers, assemblers, and transcript analysis software. In package managers it sits in the genomics CLI niche beside aligners such as BWA-MEM, Bowtie2, BLASR, NGMLR, and GMAP, with its reputation tied to speed, accuracy, and long-read versatility.

来源

• https://academic.oup.com/bioinformatics/article/34/18/3094/4994778
• https://arxiv.org/abs/1708.01492
• https://galaxyproject.org/news/2017-11-04minimap2/
• https://github.com/lh3/minimap2