菜单
mlst — chromosomal multilocus sequence typing of assemblies against PubMLST schemes (Torsten Seemann wrapper). Use for isolate / HQ-MAG species ST calling. Upstream: https://github.com/tseemann/mlst. Route via cge-finders / microbial-mining for isolate packages; plasmid ST → pmlst (different schemes).
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 mlst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 | mlst |
| description | mlst — chromosomal multilocus sequence typing of assemblies against PubMLST schemes (Torsten Seemann wrapper). Use for isolate / HQ-MAG species ST calling. Upstream: https://github.com/tseemann/mlst. Route via cge-finders / microbial-mining for isolate packages; plasmid ST → pmlst (different schemes). |
| license | MIT |
| category | analysis-tools |
| tags | ["MLST","PubMLST","typing","isolate","ST","epidemiology"] |
| upstream | https://github.com/tseemann/mlst |
| stage | mining |
Upstream: tseemann/mlst · schemes from PubMLST
Seemann, T. mlst: scan contig files against PubMLST typing schemes. https://github.com/tseemann/mlst
Jolley, K. A., Bray, J. E. & Maiden, M. C. J. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 3, 124 (2018). https://doi.org/10.12688/wellcomeopenres.14826.1
See also docs/references.md and pmlst.
Chromosomal MLST assigns a species-scheme sequence type from seven (or
scheme-defined) housekeeping loci. Auto-scheme detection can mis-assign on
novel/environmental genomes — verify species/--scheme. Novel alleles yield
incomplete STs.
Not plasmid typing (pmlst) and not ANI taxonomy (gtdbtk / skani).
Use with CGE Finders for One-Health isolate reports: species ST + resistome +
plasmids.
mamba install -c bioconda -c conda-forge mlst
mlst assembly.fasta > mlst.tsv
mlst --scheme ecoli assembly.fasta
# update schemes per upstream / mlst --list
Pin mlst version and PubMLST scheme download date.
Sequence type needed?
├─ Chromosomal PubMLST ST → mlst
├─ Plasmid scheme ST → pmlst
├─ Species/taxonomy for MAGs → gtdbtk
└─ AMR / plasmids / virulence → cge-finders / abricate / rgi
pmlst · cge-finders · abricate · staramr · plasmidfinder ·
gtdbtk · microbial-mining · tool-selection