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bedrock.bio

refseq.assembly_summary

import bedrock_bio as bb

rel = bb.load_table('refseq.assembly_summary')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession bioproject_accession biosample_accession wgs_master_accession is_historical version_status refseq_exclusion_reason assembly_not_live_date is_reference ... assembly_replicon_count assembly_scaffold_count assembly_contig_count annotation_provider annotation_name annotation_date total_gene_count protein_coding_gene_count non_coding_gene_count pubmed_ids
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 PRJNA164 SAMN02803731 None False latest None NaT True ... 7 1869 2441 FlyBase FlyBase Release 6.54 2023-12-26 17872 13962 3543 [10731132, 12537568, 12537572, 12537573, 12537...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 PRJNA168 NaN None True replaced None 2014-02-03 False ... 24 249 350 NCBI RefSeq GCF_000001405.25-RS_2024_09 2024-09-02 45350 19401 9640 [7219534, 10508508, 10591208, 10830953, 112370...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.40 PRJNA168 NaN None False latest None NaT True ... 24 470 996 NCBI RefSeq GCF_000001405.40-RS_2025_08 2025-08-01 59792 20076 22235 [7219534, 10508508, 10830953, 11237011, 117800...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001635.20 PRJNA169 NaN None True replaced None 2012-10-02 False ... 21 162 605 NCBI RefSeq Annotation submitted by NCBI RefSeq 2012-02-23 35771 21847 4338 [12954771, 19468303, 21750661]
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001635.27 PRJNA169 NaN None False latest None NaT True ... 21 101 305 NCBI RefSeq GCF_000001635.27-RS_2024_02 2024-02-01 50763 22198 17705 [12954771, 19468303, 21750661]

Description

Section titled “Description”

Selected current and historical RefSeq genome assemblies, one row per assembly.

assembly_name is NCBI’s human-readable asm_name label and may not be globally unique.

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Source provenance for the row.
assembly_accession TEXT Versioned RefSeq assembly accession (GCF accession).
bioproject_accession TEXT NCBI BioProject accession associated with the assembly, if supplied.
biosample_accession TEXT NCBI BioSample accession associated with the assembly, if supplied.
wgs_master_accession TEXT GenBank Nucleotide accession and version for the Whole Genome Shotgun project master record, if applicable. Complete-genome and clone-based assemblies do not have a WGS master record.
is_historical BOOLEAN Whether this row originated from NCBI’s historical, rather than current, RefSeq assembly summary.
version_status TEXT NCBI status of the assembly version, such as latest, replaced, suppressed, or withdrawn.
refseq_exclusion_reason TEXT NCBI excluded_from_refseq reason for exclusion from RefSeq, if applicable.
assembly_not_live_date DATE Date NCBI marked the assembly as no longer live, if applicable.
is_reference BOOLEAN Whether NCBI designates the assembly as that species’ RefSeq reference genome.
organism_taxon_id TEXT Opaque string NCBI taxonomy ID assigned to the organism represented by this assembly; maps to registry.taxa.taxon_id.
species_taxon_id TEXT Opaque string NCBI taxonomy ID assigned to the assembly’s species; joins to Ensembl taxonomy_id.
organism_name TEXT Scientific organism name reported by NCBI.
infraspecific_names STRUCT(type TEXT, name TEXT)[] Infraspecific names reported by NCBI, parsed into type and name pairs, such as strain, breed, cultivar, or ecotype.
isolate TEXT Isolate name reported by NCBI, if supplied.
assembly_level TEXT Assembly completeness classification reported by NCBI.
release_type TEXT Release classification reported by NCBI.
genome_representation TEXT Extent of genome representation reported by NCBI.
sequence_release_date DATE Date the assembly sequence was released in an INSDC database (DDBJ, ENA, or GenBank).
assembly_name TEXT NCBI asm_name: a readable assembly label, including its patch where applicable (for example, GRCh38.p14).
assembly_submitter TEXT Organization or individual that submitted the assembly.
genbank_assembly_accession TEXT Paired GenBank assembly accession (GCA accession with version), if NCBI provides one.
is_identical_to_genbank BOOLEAN Whether NCBI reports the paired GenBank assembly as identical; null when no comparison is available.
assembly_url TEXT NCBI directory URL for the RefSeq assembly package and its annotation and sequence files.
relation_to_type_material TEXT Relationship of the organism to type material reported by NCBI, if supplied.
assembly_type TEXT Ploidy or assembly type reported by NCBI, if supplied.
organism_group TEXT NCBI organism group, if supplied.
assembly_size BIGINT Total assembly length in base pairs, if supplied.
assembly_size_ungapped BIGINT Total ungapped assembly length in base pairs, if supplied.
assembly_gc_fraction FLOAT Assembly GC content as a fraction from 0 through 1, if supplied.
assembly_replicon_count INT Number of replicons in the assembly, if supplied.
assembly_scaffold_count INT Number of scaffolds in the assembly, if supplied.
assembly_contig_count INT Number of contigs in the assembly, if supplied.
annotation_provider TEXT Organization that supplied the current annotation, if supplied.
annotation_name TEXT NCBI annotation release name or version, if supplied.
annotation_date DATE Date of the current annotation release, if supplied.
total_gene_count INT Total annotated gene count, if supplied.
protein_coding_gene_count INT Protein-coding annotated gene count, if supplied.
non_coding_gene_count INT Non-coding annotated gene count, if supplied.
pubmed_ids TEXT[] PubMed identifiers associated with the assembly.