# 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

```sh
sudo av install brew:minigraph
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install minigraph
```

  Evidence: local Homebrew formula metadata

## Package facts

- **Package key:** brew:minigraph
- **Package manager:** Homebrew
- **Version:** 0.21
- **Source summary:** Proof-of-concept seq-to-graph mapper and graph generator
- **Homepage:** <https://lh3.github.io/minigraph>
- **Repository:** <https://github.com/lh3/minigraph>
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- minigraph (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 0.21
## 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 Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals


## Combined YAML source

View the package source record on GitHub. [combined/minigraph.yml](https://github.com/mxcl/pkgdb/blob/main/combined/minigraph.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- cross-ecosystem install command graph