Available columns
atb query --columns accepts the names below, and atb columns prints the same list from the CLI. Names are case-sensitive, and an unrecognised name is an error, so a typo stops the query instead of producing a blank column.
A column marked no under In index is not held in the SQLite index. Asking for one sends the query to the parquet files, which is slower and needs that file downloaded.
assembly.parquet
| Column |
In index |
Description |
sample_accession |
yes |
BioSample accession identifying the sample |
run_accession |
yes |
ENA run accession the assembly was built from |
assembly_accession |
yes |
ENA assembly accession, NA when not submitted |
sylph_species |
yes |
Species assigned by sylph against GTDB r214 |
scientific_name |
yes |
Species name as recorded by the submitter |
hq_filter |
yes |
PASS when the sample meets the high-quality criteria |
dataset |
yes |
Release the sample first appeared in |
asm_fasta_on_osf |
yes |
1 when the assembly FASTA is hosted on OSF |
aws_url |
yes |
S3 URL of the assembly FASTA |
osf_tarball_url |
yes |
OSF URL of the tarball holding the assembly |
assembly_stats.parquet
| Column |
In index |
Description |
total_length |
yes |
Total assembly length in base pairs |
number |
yes |
Number of contigs |
mean_length |
no |
Mean contig length in base pairs |
longest |
no |
Longest contig length in base pairs |
shortest |
no |
Shortest contig length in base pairs |
N50 |
yes |
Contig length at which half the assembly sits in longer contigs |
N90 |
yes |
Contig length at which 90% of the assembly sits in longer contigs |
checkm2.parquet
| Column |
In index |
Description |
Completeness_General |
yes |
Estimated completeness percentage, general model |
Contamination |
yes |
Estimated contamination percentage |
Completeness_Specific |
no |
Estimated completeness percentage, lineage-specific model |
Genome_Size |
yes |
Predicted genome size in base pairs |
GC_Content |
yes |
Fraction of G and C bases |
sylph.parquet
| Column |
In index |
Description |
Adjusted_ANI |
no |
Nucleotide identity to the species reference, coverage-adjusted |
Taxonomic_abundance |
no |
Percentage of the sample's cells estimated to be the species |
Sequence_abundance |
no |
Percentage of the sample's reads assigned to the species |
Median_cov |
no |
Median k-mer coverage of the species reference |
mlst.parquet
| Column |
In index |
Description |
mlst_scheme |
yes |
MLST scheme applied, - when the species has none |
mlst_st |
yes |
Sequence type assigned by the scheme |
mlst_status |
yes |
Typing outcome: PERFECT, NOVEL, OK or NONE |
mlst_score |
yes |
Typing confidence score out of 100 |
mlst_alleles |
yes |
Per-locus allele calls, semicolon separated |
ena_20250506.parquet
| Column |
In index |
Description |
country |
no |
Country the sample was collected in |
collection_date |
no |
Collection date, often only a year or month |
instrument_platform |
no |
Sequencing platform |
instrument_model |
no |
Sequencing instrument model |
read_count |
no |
Number of reads in the run |
base_count |
no |
Number of bases in the run |
library_strategy |
no |
Library preparation strategy |
study_accession |
no |
ENA study accession |
fastq_ftp |
no |
FTP URLs of the FASTQ files |
See also: Output formats for how to control the output format and Fetching & indexing data for how these parquet files are downloaded.