Summary statistics

Use atb summarise to count and group genomes in the database or in a previous query result.

Summarise the database

# Default summary of the full database
atb summarise

# Group by species (top 20)
atb summarise --by sylph_species --top 20

# Summarise a previous query result
atb query --genus Salmonella --hq-only --limit 100 \
  --columns sample_accession,sylph_species,hq_filter,dataset -o salmonella.tsv
atb summarise --from salmonella.tsv

# Pipe query to summarise
atb query --species "Escherichia coli" --hq-only --limit 200 \
  --columns sample_accession,sylph_species,dataset --format csv | \
  atb summarise --from -

Related pages

• Fetching & indexing data — download the database before running atb summarise
• Querying genomes — filter genomes to feed into atb summarise --from