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bio-epidemiological-genomics-pathogen-typing
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epidemiological-genomics-pathogen-typing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: mlst assembly.fasta for 7-gene MLST typing.
- CLI: chewBBACA.py AlleleCall for core genome MLST (cgMLST).
- 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).
- conda install -c bioconda mlst.
Source Doc
Excerpt From SKILL.md
Specify scheme
mlst --scheme senterica genome.fasta
Include allele sequences in output
mlst --csv genome.fasta > results.csv
## Download or create schema
chewBBACA.py DownloadSchema -sp "Salmonella enterica" -o schema_dir
Use cases
- Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- epidemiological-genomics/phylodynamics - Time-scaled trees from typed isolates
- epidemiological-genomics/transmission-inference - Outbreak investigation
- metagenomics/kraken-classification - Species identification
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