mlstdb

Keep your mlst databases up to date. mlstdb handles OAuth authentication with PubMLST and BIGSdb Pasteur so you can download the latest MLST schemes and build a BLAST database, in two commands.

Full Documentation

Install

conda create -n mlst -c bioconda mlst
conda activate mlst
pip install mlstdb

Other installation methods

# From bioconda (include conda-forge for dependencies)
conda install -c conda-forge -c bioconda mlstdb

# Or install both tools together
conda create -n mlst -c conda-forge -c bioconda mlst mlstdb

# From PyPI only
pip install mlstdb

Quick Start

1. Register with each database (one-time setup):

mlstdb connect --db pubmlst
mlstdb connect --db pasteur

This opens a browser for OAuth registration. Follow the prompts to authorise mlstdb.

2. Download schemes and build the BLAST database:

mlstdb update

This downloads the curated MLST schemes from both PubMLST and Pasteur and creates a BLAST database.

3. Use with mlst:

mlst --blastdb blast/mlst.fa --datadir pubmlst your_assembly.fasta

That's it. For advanced scheme exploration, custom filtering, and detailed option reference, see the full documentation.

Caution

• Back up your existing MLST databases before running updates.
• Curate your scheme list before updating — not all schemes are validated for the mlst tool.
• The mlst tool is designed for bacterial species only.

Acknowledgements

Built upon the work of:

• BIGSdb_downloader by Keith Jolley
• pyMLST by Benoit Valot

License

mlstdb was previously licensed under MIT. As of version 0.1.7, it is licensed under GPL v3. Original MIT‑licensed code is preserved and attributed according to MIT terms.

For additional support, please raise an issue.