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Atb

atb

Query and download AllTheBacteria genomes

Options

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)
  -h, --help              help for atb

SEE ALSO

  • atb agc - Download and inspect genomes in AGC archives
  • atb amr - Query AMR gene data
  • atb config - Manage atb configuration
  • atb download - Download genome assemblies
  • atb fetch - Download ATB parquet metadata tables
  • atb index - Build or rebuild the SQLite query index
  • atb info - Show detailed information for a sample
  • atb mcp - Start MCP server for LLM integration
  • atb mlst - Query MLST (Multi-Locus Sequence Typing) data for bacterial genomes
  • atb osf - Browse and download files from the AllTheBacteria OSF repository
  • atb query - Query the ATB database
  • atb sketch - Find closest ATB genomes using sketch distances
  • atb summarise - Print summary statistics for the ATB database
  • atb update - Update atb to the latest version
  • atb version - Print version and environment information