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.
Profile →npx skills add majiayu000/claude-skill-registry --skill 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.
# Pathogen Typing ## 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 > results.csv ``` ## Parse MLST Results ```python import pandas as pd import subprocess def run_mlst(fasta_files, scheme=None): '''Run MLST on multiple genomes Returns DataFrame with: - Sample name - Scheme (auto-detected or specified) - Sequence type (ST) - Allele profiles ST interpretation: - Known ST: Matches existing type in database - Novel allele: New allele combination, may be unreported ST - Failed: Unable to determine (poor assembly or wrong scheme) ''' cmd = ['mlst'] + fasta_files if scheme: cmd.extend(['--scheme', scheme]) result = subprocess.run(cmd, capture_output=True, text=True) lines = result.stdout.strip().split('\n') data = [line.split('\t') for line in lines] return pd.DataFrame(data, columns=['file', 'scheme', 'ST'] + [f'locus{i}' for i in range(1, len(data[0])-2)]) ```
- 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 majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.