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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-metagenomics-strain-tracking
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-strain-tracking
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: mash dist, sourmash compare, fastANI, inStrain profile.
- Track bacterial strains across my samples" → Resolve sub-species variation using genome sketching (Mash/sourmash), average nucleotide identity (fastANI), or within-sample strain profiling (inStrain) for outbreak tracking and transmission analysis. CLI: mash dist, sourmash compare, fastANI, inStrain profile.
- Identify and track bacterial strains at sub-species resolution.
- mash sketch -o genome.msh genome.fasta.
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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