菜单
Fast robust average nucleotide identity (ANI) for metagenomic genomes and MAG comparisons. Use for species-level clustering, novelty vs GTDB/UHGG, and scalable ANI matrices. Upstream: https://github.com/bluenote-1577/skani.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill skani命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
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正在显示 SKILL.md
| name | skani |
| description | Fast robust average nucleotide identity (ANI) for metagenomic genomes and MAG comparisons. Use for species-level clustering, novelty vs GTDB/UHGG, and scalable ANI matrices. Upstream: https://github.com/bluenote-1577/skani. |
| license | MIT |
| category | analysis-tools |
| tags | ["ANI","comparative-genomics","MAG"] |
| upstream | https://github.com/bluenote-1577/skani |
| stage | binning |
Upstream: bluenote-1577/skani
Shaw, J. & Yu, Y. W. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat. Methods 20, 1661–1665 (2023). https://doi.org/10.1038/s41592-023-02018-3
skani estimates ANI quickly on incomplete MAGs better than many classic tools that assume near-complete genomes. Use for:
drep · fastanimgnify)95% ANI remains a common species-level heuristic — state your cutoff.
skani | fastani | |
|---|---|---|
| Strength | Speed/robustness on incomplete MAGs; large catalogues | Classic literature-compatible ANI |
| Prefer | New large MAG studies | Reproducing FastANI-based Methods |
| Skill | this | fastani |
Do not mix FastANI and skani values in one unlabeled matrix.
conda install -c bioconda skani
# Sketch + triangle / dist
skani triangle bins_hq/*.fa > temp/ani/skani.triangle
skani dist bins_hq/query.fa bins_hq/*.fa > temp/ani/query_vs_all.tsv
fastani · drep · gtdb · mgnify · checkm2 · gtdbtk · mag-qc