Command line tool

The atb command line tool is the recommended way to query AllTheBacteria metadata, download assemblies, browse OSF files, search AMR/MLST results, and query the sketchlib index. It uses the aggregated data up to and including incremental release 2025-05.

The full command reference is maintained with the tool: https://allthebacteria.github.io/atb-cli/.

Install

On Linux or macOS:

curl -fsSL https://raw.githubusercontent.com/allthebacteria/atb-cli/main/install.sh | bash

Pre-built binaries for Linux, macOS, and Windows are available from: https://github.com/allthebacteria/atb-cli/releases/latest.

First use

Choose a data directory on a disk with enough space. The default metadata fetch includes AMR data and builds local indexes; this can use roughly 35 GB. Add another few GB if you fetch the sketchlib index.

atb config set general.data_dir /path/to/large/volume/atb-data
atb fetch
atb query --species "Escherichia coli" --hq-only --limit 10

If you do not need AMR queries, fetch only the core non-AMR tables:

atb fetch --tables assembly.parquet,assembly_stats.parquet,checkm2.parquet,sylph.parquet,run.parquet,mlst.parquet

Common tasks

Query genomes and select useful columns:

atb query --species "Klebsiella pneumoniae" --hq-only \
  --columns sample_accession,sylph_species,N50,Completeness_General,aws_url \
  --limit 20

Download assemblies from a query:

atb query --species "Escherichia coli" --hq-only \
  --columns sample_accession,aws_url --limit 10 -o ecoli.tsv
atb download --from ecoli.tsv --output-dir ./ecoli_genomes

Browse and download files from OSF:

atb osf ls
atb osf ls AMR
atb osf download --verify "AMRFinderPlus.*latest"

Query AMRFinderPlus results:

atb amr --species "Escherichia coli" --class "BETA-LACTAM" --hq-only
atb amr --gene "blaCTX-M-15" --limit 100

Query MLST calls:

atb mlst --species "Escherichia coli" --st 131 --hq-only
atb mlst --scheme salmonella --limit 50

Find closest genomes with sketchlib:

atb sketch install
atb sketch fetch
atb sketch query my_genome.fasta --knn 50

The CLI installs sketchlib v0.2.4 when you run atb sketch install. The ATB sketch database used by the website documentation is the aggregated 2025-05 sketchlib index.

When to use manual methods

The manual OSF, AWS, ENA, and SQLite instructions in these docs are kept for power users who need exact archive paths, direct database access, custom pipelines, or reproducible low-level commands. For routine querying and downloads, start with atb.

Overview Metadata and QC