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gmlst

gmlst is a fast Python 3.12 CLI for bacterial genome typing with classical MLST, large cgMLST and wgMLST schemes, and scheme-free discovery workflows.

Features

  • Broad typing support: mlst, cgmlst, and tgmlst from the same CLI
  • Multiple backends: BLAST+, KMA, minimap2, MUMmer4, and a pure-Python kmer-hash engine
  • FASTA and FASTQ input: assembled genomes and paired-end raw reads
  • Multiple providers: PubMLST, Pasteur BIGSdb, Enterobase, cgmlst.org, and local custom schemes
  • Novel allele workflow: detect novel alleles, extract profiles, build custom databases
  • Scheme-free typing: de novo allele discovery without a preselected scheme
  • Local visualization: Flask + Vue web app with MST visualization

Quick Start

# Install
pip install gmlst

# List and download a scheme
gmlst scheme list
gmlst scheme download saureus_1

# Type a sample
gmlst typing mlst -s saureus_1 sample.fasta

Documentation

English

Section Description
Installation Setup and environment
Quick Start First-run workflow
Commands CLI reference
Backends Alignment backends
Providers Data sources
Configuration Environment variables
cgMLST Guide cgMLST modes
Novel Workflow Novel allele pipeline
Visualization MST visualization
FAQ Troubleshooting

简体中文

章节 说明
安装 安装与环境配置
快速入门 首次运行流程
后端 比对后端
数据源 数据来源
配置参考 环境变量
cgMLST 指南 cgMLST 模式
Novel 工作流 新等位基因流程
可视化 MST 可视化
FAQ 常见问题