macOS
Homebrewverified · 100%
brew install minimap2local Homebrew formula metadata
brew
Install minimap2 with Homebrew, apt, Nix
Versatile pairwise aligner for genomic and spliced nucleotide sequences. Version 2.31 via Homebrew; verified 2026-05-20.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install libminimap2-devDebian stable package indexes · libminimap2-dev · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#minimap2nixpkgs package indexes · pkgs/by-name/mi/minimap2/package.nix · source: api.github.com
overview
Package summary
Versatile pairwise aligner for genomic and spliced nucleotide sequences
Project links
Commands and aliases
- minimap2
- sdust
history
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 posture
No protected-tool coverage found yet
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.
Install behavior
- No Homebrew post-install hook is recorded in formula metadata.
- Homebrew bottle metadata is available for 6 platform targets.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
minimap2 | cli | global executable | |
sdust | cli | global executable |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-07-08
manager version2.31
manager updated2026-05-20
local dataok
upstreamcurrent
latest detectedv2.31
https://github.com/lh3/minimap2
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:minimap2 |
|---|---|
| Version | 2.31 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/minimap2 |
| Homepage | https://lh3.github.io/minimap2 |
| Repository | https://github.com/lh3/minimap2 |
| Upstream docs | https://lh3.github.io/minimap2/minimap2.html |
| License | MIT |
| Source archive | https://github.com/lh3/minimap2/archive/refs/tags/v2.31.tar.gz |
| Last updated | 2026-05-20T00:41:23Z |
| Pulse | updated |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | minimap2 |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
libminimap2-dev 2.27+dfsg-1+b3
development headers for libminimap
https://github.com/lh3/minimap2
sudo apt install libminimap2-dev- Section: libdevel
- Architecture: amd64
- Source Package: minimap2
- 1 dependencies
- normalized package name match
- Matched by: Minimap2
Debian apt95%
minimap2 2.27+dfsg-1+b3
versatile pairwise aligner for genomic and spliced nucleotide sequences
https://github.com/lh3/minimap2
sudo apt install minimap2- Section: science
- Architecture: amd64
- Source Package: minimap2
- 2 dependencies
- normalized package name match
- Matched by: Minimap2
Debian apt95%
python3-mappy 2.27+dfsg-1+b3
Python3 interface minimap2
https://github.com/lh3/minimap2
sudo apt install python3-mappy- Section: python
- Architecture: amd64
- Source Package: minimap2
- 3 dependencies
- normalized package name match
- Matched by: Minimap2
Nix95%
minimap2
nix profile install nixpkgs#minimap2- normalized package name match
- Matched by: Minimap2
Ubuntu apt95%
libminimap2-dev 2.26+dfsg-1build1
development headers for libminimap
https://github.com/lh3/minimap2
sudo apt install libminimap2-dev- Section: universe/libdevel
- Architecture: amd64
- Source Package: minimap2
- 1 dependencies
- normalized package name match
- Matched by: Minimap2
Ubuntu apt95%
minimap2 2.26+dfsg-1build1
versatile pairwise aligner for genomic and spliced nucleotide sequences
https://github.com/lh3/minimap2
sudo apt install minimap2- Section: universe/science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Minimap2
Ubuntu apt95%
python3-mappy 2.26+dfsg-1build1
Python3 interface minimap2
https://github.com/lh3/minimap2
sudo apt install python3-mappy- Section: universe/python
- Architecture: amd64
- Source Package: minimap2
- 3 dependencies
- normalized package name match
- Matched by: Minimap2
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment