bio-metagenomics-strain-tracking
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-strain-tracking --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Bowtie2 2.5.3+, MetaPhlAn 4.1+, numpy 1.26+, pandas 2.2+, samtools 1.19+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Strain Tracking **"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. ## 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 | SN
- Version Compatibility
- Tool Comparison
- MASH
- Installation
- Create Sketch
- Calculate Distance
- Interpret MASH Distance
- Cluster Genomes
- sourmash
- Create Signatures
- Compare Signatures
- Taxonomy Assignment
- fastANI
- Calculate ANI
conda install -c bioconda mash Single genome mash sketch -o genome.msh genome.fasta 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 Pairwise distance mash dist genome1.fasta genome2.fasta Query against database
What does the bio-metagenomics-strain-tracking skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-strain-tracking --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.