使用 Homebrew 安装 minigraph

项目链接

• 主页
• 仓库

命令和别名

• minigraph

项目历史

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.

使用方式

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.

来源

• 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/