Downloading assemblies

Use atb download to save genome FASTA files to disk, either from a query results file or directly from URLs.

Download genomes

# Query, then download
atb query --species "Klebsiella pneumoniae" --hq-only --limit 10 \
  --columns sample_accession,aws_url --format csv -o results.csv
atb download --from results.csv --output-dir ./genomes

# Pipe query directly to download
atb query --species "Escherichia coli" --hq-only --limit 5 \
  --columns sample_accession,aws_url --format csv | \
  atb download --from - --output-dir ./ecoli_genomes

# Preview what would be downloaded
atb download --from results.csv --dry-run

# Download from a URL list
atb download --urls my_urls.txt --output-dir ./genomes --parallel 8

# Download a single file
atb download --url https://allthebacteria-assemblies.s3.eu-west-2.amazonaws.com/SAMD00000355.fa.gz \
  --output-dir ./genomes

Genomes are saved to --output-dir when given, otherwise to download.output_dir (default ~/atb/genomes). That is a separate location from the metadata directory (general.data_dir / --data-dir / $ATB_DATA_DIR), so the data-dir setting does not change where downloads land.

Samples with no assembly

Around 464,000 samples in ATB have no assembly. Their aws_url is the literal string NA. atb download --from skips those rows and reports the count:

Skipping 1065 row(s) with no assembly (aws_url is NA)
Downloading 4775 file(s) to /home/ubuntu/atb/genomes

To leave them out of the query results in the first place, add --has-assembly:

atb query --species "Escherichia coli" --has-assembly \
  --columns sample_accession,aws_url -o results.tsv

Related pages

• Querying genomes — filter and select genomes to feed into atb download
• AMR genes — use --download to fetch assemblies for AMR-matched samples
• MLST — use --download to fetch assemblies for MLST-matched samples
• Finding closest genomes — use --download to fetch assemblies for sketch-matched genomes