query

atb sketch query

Find closest ATB genomes for your input sequences

Synopsis

Sketch your input FASTA file(s) and find the closest matches in the AllTheBacteria sketch database. Results include ANI (Average Nucleotide Identity) and metadata from the local ATB index.

atb sketch query <fasta> [fasta...] [flags]

Examples

  # Find 10 closest genomes (default)
  atb sketch query my_genome.fasta

  # Top 50 closest
  atb sketch query my_genome.fasta --knn 50

  # Multiple input files
  atb sketch query sample1.fasta sample2.fasta

  # Batch from file list (one path per line)
  atb sketch query -f input_list.txt

  # Raw sketchlib distances without metadata enrichment
  atb sketch query my_genome.fasta --raw

  # Find closest and download their assemblies
  atb sketch query my_genome.fasta --download ./closest_genomes

  # Preview downloads without actually downloading
  atb sketch query my_genome.fasta --download ./closest_genomes --dry-run

Options

      --download string    download matched genomes to this directory
      --dry-run            show what would be downloaded without downloading
  -f, --file-list string   file with one FASTA path per line
      --format string      output format: tsv, csv, json, table (default: auto)
  -h, --help               help for query
      --knn int            number of closest matches to return (default 10)
      --raw                output raw distances without metadata enrichment
      --threads int        CPU threads (default: all cores minus one)

Options inherited from parent commands

      --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)

SEE ALSO

• atb sketch - Find closest ATB genomes using sketch distances