菜单
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.
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 genomad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。
基于 SOC 职业分类
正在显示 SKILL.md
| 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