atb-cli

atb-cli (the atb command) queries the AllTheBacteria genomics database (~3.2M bacterial genomes), searches AMR / stress / virulence genes, finds the closest genomes via sketch distances, and downloads genome assemblies — all from your terminal. It ships as a single binary with no dependencies, and reads the project's Parquet metadata through a fast local index, so most queries return in milliseconds.

Supported platforms: Linux, macOS, Windows (amd64 and arm64).

What you can do

• Query genomes by species, quality, geography, sequencing platform, and date.
• Search resistance, stress, and virulence genes (AMRFinderPlus) and MLST types.
• Find the closest genomes to your own assembly across ~3.2M genomes.
• Download assemblies for any query result, with preview and parallelism controls.
• Browse and fetch the underlying data files from OSF.
• Drive it from an LLM through the built-in MCP server.

Get started

1. Install atb-cli
2. Quick start — download the database and run your first query
3. Work through the guides for task-by-task walkthroughs
4. Look up exact flags in the CLI reference

Credits

atb-cli was designed and architected by Thanh Le Viet in his personal capacity, using his own Claude account. The implementation was developed with coding assistance from Claude (Anthropic) under human direction and review. Thanks to hackathon participants Jane Hawkey, Ahmed M Moustafa, Martin Hunt, and Zamin Iqbal for their input and feedback.

Released under the MIT License.