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, andtgmlstfrom 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 -s saureus_1
# Type a sample
gmlst typing mlst -s saureus_1 sample.fasta
Documentation¶
| Section | Description |
|---|---|
| Installation | Setup and environment |
| Quick Start | First-run workflow |
| Commands | CLI reference |
| Backends | Alignment backends |
| Providers | Data sources |
| cgMLST Guide | cgMLST modes |
| Novel Workflow | Novel allele pipeline |
| Visualization | MST visualization |
| FAQ | Troubleshooting |