A command-line tool for querying the AllTheBacteria genomics database (~3.2M bacterial genomes), searching AMR/stress/virulence genes, finding closest genomes via sketch distances, and downloading genome assemblies.
Single binary, no dependencies.
Supported platforms: Linux, macOS, Windows (amd64 and arm64)
Full documentation: https://allthebacteria.github.io/atb-cli/ (also on Read the Docs)
One-line install (Linux/macOS):
curl -fsSL https://raw.githubusercontent.com/allthebacteria/atb-cli/main/install.sh | bashPre-built binaries for all platforms are also available on the releases page.
See the installation guide for all methods.
# 1. Download the database (~540 MB core tables)
atb fetch
# 2. Query
atb query --species "Escherichia coli" --hq-only --limit 10See the quick start guide for next steps.
- Guides — querying genomes, AMR, MLST, sketch distances, downloads, and more
- CLI reference — every command and flag
- LLM integration (MCP) — use
atbas an MCP server with Claude, ChatGPT, Cursor, and others
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), an AI assistant that helped with code generation, testing, and documentation under human direction and review. Thanks to hackathon participants Jane Hawkey, Ahmed M Moustafa, Martin Hunt, and Zamin Iqbal for their input and feedback.