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Identify plasmids, viruses, and other mobile genetic elements in assemblies or genomes. Use for plasmidome/virome mining, MGE-aware AMR context, and pre-CheckV viral candidate lists. Upstream: https://github.com/apcamargo/genomad.
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 genomad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 | genomad |
| description | Identify plasmids, viruses, and other mobile genetic elements in assemblies or genomes. Use for plasmidome/virome mining, MGE-aware AMR context, and pre-CheckV viral candidate lists. Upstream: https://github.com/apcamargo/genomad. |
| license | MIT |
| category | analysis-tools |
| tags | ["MGE","plasmid","virus","genome-mining"] |
| upstream | https://github.com/apcamargo/genomad |
| stage | mining |
Upstream: apcamargo/genomad
Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303–1312 (2024). https://doi.org/10.1038/s41587-023-01953-y
geNomad scores contigs/genomes for plasmid-like and virus-like signals using markers + neural networks. Use it to:
checkvrgi hits on plasmid contigs)Do not equate “plasmid score high” with a complete circular plasmid. For viruses,
always run CheckV before publishing vMAG completeness. For finer MGE detail
use mobileog (proteins), isescan (IS), integronfinder (integrons), and
mob-suite (MOB/replicon typing) or plasmidfinder / staramr (CGE replicons).
Can run on full assemblies (pre-binning) or on bins; pre-binning catches MGEs that never enter bacterial bins.
| Requirement | Minimum | Recommended |
|---|---|---|
| DB | genomad download-database | Pin path + version |
| Input | Contigs or genomes FASTA | |
| CPU | 8 | 16+ |
| Disk | DB tens of GB class | SSD helpful |
conda install -c bioconda genomad
genomad download-database db/genomad
genomad end-to-end \
contigs.fa \
temp/genomad/${id} \
-d db/genomad \
--threads 16 \
--cleanup
# Key tables (names may include sample prefix)
# temp/genomad/${id}/${id}_summary/${id}_virus_summary.tsv
# temp/genomad/${id}/${id}_summary/${id}_plasmid_summary.tsv
| Option | Guidance |
|---|---|
--splits | Lower memory on huge assemblies (see docs) |
--cleanup | Remove intermediate heavy files |
| score cutoffs | Filter summary TSVs for reporting |
MGE / virus goal?
├─ Plasmid + virus screen on assembly → genomad
├─ Virus-focused legacy SOP → virsorter2 (± genomad consensus)
└─ Publish viral genomes → checkv quality mandatory
| Symptom | Action |
|---|---|
| DB path errors | Absolute path to downloaded DB |
| Memory errors | --splits / smaller input chunks |
| Empty virus table | Low viral signal or too-short contigs — check min length filters |
checkv · virsorter2 · vcontact · plasmaag · mobileog · isescan ·
integronfinder · mob-suite · cge-finders · plasmidfinder · staramr ·
rgi · resfinder · antismash · microbial-mining · megahit