メニュー
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.
デフォルトでは、最初にソースを確認する Prompt が選択されています。直接コマンドに切り替えるか、ローカルコピーをダウンロードすることもできます。
インストールを決める前に、SKILL.md と SkillsMP に表示されている付属ファイルをお読みください。
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
直接コマンドでは確認用 Prompt が省略されます。実行前にソースを確認してください。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill skaniコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
ローカルで確認しますか？SkillsMP が現在取得できるファイルをダウンロードできます。
ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks. Upstream: https://github.com/tseemann/abricate. Route via cge-finders / microbial-mining; official CGE CLI still via resfinder/plasmidfinder when phenotype mapping or PointFinder is required.
Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for clinical/One-Health isolate typing and plasmid-borne AMR context — not community-wide dark-matter discovery. Child skills: plasmidfinder, resfinder, pointfinder, disinfinder, virulencefinder, mobileelementfinder, pmlst, staramr, abricate, mlst. Complements genomad, mob-suite, rgi, mobileog. Route via microbial-mining.
DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db. Route via cge-finders / resfinder / microbial-mining.
SOC 職業分類に基づく
SKILL.md を表示中
| 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