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数据与复现
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bio-metagenomics-strain-tracking
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-strain-tracking
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- CLI：mash dist，sourmash compare，fastANI，inStrain profile。
- 跟踪 bacterial strains across my samples" → Resolve sub-species variation ，使用 genome sketching (Mash/sourmash)，average nucleotide identity (fastANI)，或 within-sample strain profiling (inStrain) ，用于 outbreak tracking 、 transmission analysis. CLI：mash dist，sourmash compare，fastANI，inStrain profile。
- Identify 、 track bacterial strains at sub-species resolution。
- mash sketch -o genome.msh genome.fasta。
原始文档
SKILL.md 摘录
Tool Comparison
| Tool | Method | Best For |
|---|---|---|
| MASH | MinHash sketches | Fast distance estimation |
| sourmash | MinHash + containment | Metagenome comparisons |
| fastANI | ANI calculation | Accurate species/strain ID |
| inStrain | SNV profiling | Strain dynamics in metagenomes |
Multiple genomes
mash sketch -o reference_db.msh genomes/*.fasta
From reads (with coverage)
mash sketch -m 2 -r -o reads.msh reads.fastq.gz
适用场景
- 适合在needing sub-species resolution ，用于 outbreak tracking，transmission analysis，或 within-host strain dynamics时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- metagenomics/kraken-classification - Taxonomic classification
- genome-assembly/contamination-detection - Contamination screening
- phylogenetics/modern-tree-inference - Phylogenetic analysis
- metagenomics/metaphlan-profiling - Species profiling
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