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brew install minigraphlocal Homebrew formula metadata
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Install minigraph with Homebrew
Proof-of-concept seq-to-graph mapper and graph generator. Version 0.21 via Homebrew; verified from local package data.
install
Additional install commands
overview
Package summary
Proof-of-concept seq-to-graph mapper and graph generator
Project links
Commands and aliases
- minigraph
history
Project history and usage
minigraph is Heng Li's sequence-to-graph mapper and pangenome graph generator. The GitHub project describes it as a tool that aligns query sequences against a sequence graph and incrementally augments that graph with long divergent subsequences; the project documentation also notes that a significant portion of the source derives from minimap2, Li's pairwise nucleotide aligner.
Project history
The tool sits in the pangenome era of bioinformatics, where multiple high-quality assemblies are represented as a graph rather than flattened into one linear reference. The 2020 Genome Biology paper by Li, Feng, and Chu introduced the design and construction of reference pangenome graphs with minigraph, including a graph-based data model and formats intended to preserve coordinates against a linear reference. The command-line workflow maps sequences to sequences or graphs, emits PAF/GAF-style mappings, builds rGFA graphs from reference and sample assemblies, and can feed structural-variation extraction through gfatools.
How it is used
Its adoption history is tied to pangenome-reference research rather than general-purpose package use. Later Minigraph-Cactus work used minigraph to construct a structural-variation graph from input assemblies before Cactus refined it into richer pangenome graph outputs, and that pipeline demonstrated scaling to 90 human haplotypes from the Human Pangenome Reference Consortium. In package managers, minigraph is a specialist bioinformatics CLI for researchers building or testing genome graphs, often alongside minimap2, gfatools, vg, Cactus, and Bioconda-style scientific software stacks.
Sources
- https://formulae.brew.sh/formula/minigraph
- https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md
- https://github.com/lh3/minigraph
- https://lh3.github.io/minigraph/
- https://link.springer.com/article/10.1186/s13059-020-02168-z
- https://profiles.wustl.edu/en/publications/pangenome-graph-construction-from-genome-alignments-with-minigrap
- https://pubmed.ncbi.nlm.nih.gov/33066802/
security posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
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 |
|---|---|---|---|
minigraph | 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 version0.21
manager updated
local dataok
upstreamcurrent
latest detectedv0.21
https://github.com/lh3/minigraph
- infoNo package-manager update timestamp was available.low confidence
install metadata
Package metadata
| Package key | brew:minigraph |
|---|---|
| Version | 0.21 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/minigraph |
| Homepage | https://lh3.github.io/minigraph |
| Repository | https://github.com/lh3/minigraph |
| Upstream docs | https://github.com/lh3/minigraph#readme |
| License | MIT |
| Source archive | https://github.com/lh3/minigraph/archive/refs/tags/v0.21.tar.gz |
| 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 | minigraph |
| 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 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
- package relationship graph
- package version freshness
- package-page enrichment