# Install minimap2 with Homebrew, apt, Nix Versatile pairwise aligner for genomic and spliced nucleotide sequences. Version 2.31 via Homebrew; verified 2026-05-20. Also installable with debian: sudo apt install libminimap2-dev. ## Install ```sh sudo av install brew:minimap2 ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install minimap2 ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install minimap2 ``` Evidence: Debian stable package indexes: minimap2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#minimap2 ``` Evidence: nixpkgs package indexes: pkgs/by-name/mi/minimap2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:minimap2 - **Package manager:** Homebrew - **Version:** 2.31 - **Source summary:** Versatile pairwise aligner for genomic and spliced nucleotide sequences - **Homepage:** - **Repository:** - **Last updated:** 2026-05-20T00:41:23Z - **Generated:** 2026-08-03T19:37:03+00:00 ## Executables - minimap2 (alias) - sdust (alias) ## Install behavior - Bottle: not available ## Freshness - Page generated: 2026-08-03 - Package-manager version: 2.31 ## Project history and usage minimap2 is Heng Li's successor to the original minimap, designed for the alignment problems created by long-read sequencing and large genomic assemblies. The 2017 preprint and 2018 Bioinformatics paper present it as a general-purpose pairwise aligner for DNA and long mRNA sequences, motivated by ultra-long reads, full-length transcript reads, and contigs that older aligners could not process efficiently at scale. ### Project history 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. ### How it is used 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. ### Sources - - - - ## Security Notes No matching local secret-handling manifest was found for minimap2. Nucleus package metadata is still published here so future coverage has a stable package URL. ## Other Package-Manager Records - Debian apt - libminimap2-dev - 2.27+dfsg-1+b3: normalized package name match | Debian stable package indexes: libminimap2-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | development headers for libminimap | https://github.com/lh3/minimap2 - Debian apt - minimap2 - 2.27+dfsg-1+b3: normalized package name match | Debian stable package indexes: minimap2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | versatile pairwise aligner for genomic and spliced nucleotide sequences | https://github.com/lh3/minimap2 - Debian apt - python3-mappy - 2.27+dfsg-1+b3: normalized package name match | Debian stable package indexes: python3-mappy from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Python3 interface minimap2 | https://github.com/lh3/minimap2 - Nix - minimap2: normalized package name match | nixpkgs package indexes: pkgs/by-name/mi/minimap2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - libminimap2-dev - 2.26+dfsg-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: libminimap2-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | development headers for libminimap | https://github.com/lh3/minimap2 - Ubuntu apt - minimap2 - 2.26+dfsg-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: minimap2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | versatile pairwise aligner for genomic and spliced nucleotide sequences | https://github.com/lh3/minimap2 - Ubuntu apt - python3-mappy - 2.26+dfsg-1build1: normalized package name match | Ubuntu 24.04 LTS package indexes: python3-mappy from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Python3 interface minimap2 | https://github.com/lh3/minimap2 ## Combined YAML source View the package source record on GitHub. [combined/minimap2.yml](https://github.com/mxcl/pkgdb/blob/main/combined/minimap2.yml) ## Sources - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph