bio-epidemiological-genomics-pathogen-typing

name	bio-epidemiological-genomics-pathogen-typing
description	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.
tool_type	cli
primary_tool	mlst

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

conda install -c bioconda mlst


mlst genome.fasta



mlst *.fasta > typing_results.tsv


mlst --scheme senterica genome.fasta


mlst --list


mlst --csv genome.fasta > results.csv