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Finding closest genomes

Use atb sketch to find the closest genomes in the ATB database to your input sequences using MinHash sketch distances via sketchlib. Results include ANI (Average Nucleotide Identity) and enriched metadata.

Linux/macOS only -- sketchlib binaries are not available for Windows.

One-time setup

  1. Install sketchlib (downloads binary next to atb): 
    atb sketch install
  2. Download the ATB sketch database (~4.2 GB): 
    atb sketch fetch

Query genomes

# 3. Query your genome against ~3.2M ATB genomes
atb sketch query my_genome.fasta

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

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

# Batch from a file list
atb sketch query -f input_list.txt

# Find closest genomes 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 --dry-run

# Raw sketchlib output (no metadata enrichment)
atb sketch query my_genome.fasta --raw

# JSON output
atb sketch query my_genome.fasta --format json

Output columns: query, sample_accession, ani, species, N50, completeness, mlst_st

When --download is used, the output directory will contain: - Downloaded genome FASTA files (.fa.gz) - sketch_results.tsv -- full query results with download URLs - manifest.json -- download summary (consistent with atb download)

# Show info about the local sketch database
atb sketch info

See Downloading assemblies for more on the --download flag and output directory options.