bio-epidemiological-genomics-pathogen-typing
Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-pathogen-typing --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: mlst 2.23+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, 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. # Pathogen Typing **"Type my bacterial isolates by MLST"** → Assign multi-locus sequence types to bacterial genomes for isolate characterization, outbreak clone identification, and strain tracking. - CLI: `mlst assembly.fasta` for 7-gene MLST typing - CLI: `chewBBACA.py AlleleCall` for core genome MLST (cgMLST) ## MLST with mlst Tool ```bash # Install mlst conda install -c bioconda mlst # Basic MLST typing mlst genome.fasta # Output: genome.fasta ecoli ST131 adk(53) fumC(40) gyrB(47) ... # Batch typing mlst *.fasta > typing_results.tsv # Specify scheme mlst --scheme senterica genome.fasta # List available schemes mlst --list # Include allele sequences in output mlst --csv genome.fasta >
- Version Compatibility
- MLST with mlst Tool
- Parse MLST Results
- Core Genome MLST (cgMLST)
- cgMLST Distance Analysis
- SNP-Based Typing
- Enterobase Integration
- Related Skills
Install mlst conda install -c bioconda mlst Basic MLST typing mlst genome.fasta Batch typing mlst *.fasta > typing_results.tsv Specify scheme mlst --scheme senterica genome.fasta List available schemes mlst --list
What does the bio-epidemiological-genomics-pathogen-typing skill do?
Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-pathogen-typing --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.