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README for the assembly_summary_genbank.txt, assembly_summary_refseq.txt and
assembly_summary.txt files found on the NCBI genomes FTP site:
https://ftp.ncbi.nlm.nih.gov/genomes
Last updated: December 30, 2024
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======================
ASSEMBLY SUMMARY FILES
======================
The assembly_summary files report metadata for the genome assemblies on the
NCBI genomes FTP site.
Four master files reporting data for either GenBank or RefSeq genome assemblies
are available under https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/
assembly_summary_genbank.txt - current GenBank genome assemblies
assembly_summary_genbank_historical.txt - replaced and suppressed GenBank genome
assemblies
assembly_summary_refseq.txt - current RefSeq genome assemblies
assembly_summary_refseq_historical.txt - replaced and suppressed RefSeq genome
assemblies
assembly_summary_genbank.txt and assembly_summary_genbank_historical.txt are
also available at:
https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank_historical.txt
assembly_summary_refseq.txt and assembly_summary_refseq_historical.txt are
also available at:
https://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
https://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq_historical.txt
The assembly_summary.txt files in the directories named for taxonomic groups or
species contain the relevant subsets of the data from the master files.
=====================
COLUMN SPECIFICATIONS
=====================
The assembly_summary.txt files have 37 tab-delimited columns.
Header rows begin with '#".
Column 1: "assembly_accession"
Assembly accession: the assembly accession.version reported in this field is
a unique identifier for the set of sequences in this particular version of
the genome assembly.
Column 2: "bioproject"
BioProject: accession for the BioProject which produced the sequences in the
genome assembly. A BioProject is a collection of biological data related to a
single initiative, originating from a single organization or from a
consortium. A BioProject record provides users a single place to find links
to the diverse data types generated for that project. The record can be
retrieved from the NCBI BioProject resource:
https://www.ncbi.nlm.nih.gov/bioproject/
Column 3: "biosample"
BioSample: accession for the BioSample from which the sequences in the genome
assembly were obtained. A BioSample record contains a description of the
biological source material used in experimental assays. The record can be
retrieved from the NCBI BioSample resource:
https://www.ncbi.nlm.nih.gov/biosample/
Column 4: "wgs_master"
WGS-master: the GenBank Nucleotide accession and version for the master
record of the Whole Genome Shotgun (WGS) project for the genome assembly. The
master record can be retrieved from the NCBI Nucleotide resource:
https://www.ncbi.nlm.nih.gov/nuccore
Genome assemblies that are complete genomes, and those that are clone-based,
do not have WGS-master records in which case this field will be empty.
Column 5: "refseq_category"
RefSeq Category: whether the assembly is a reference genome in the NCBI
Reference Sequence (RefSeq) project classification.
Values:
reference genome - a genome computationally or manually selected
as a reference for the species.
na - no RefSeq category assigned to this assembly
Details of the selection of reference are at:
https://www.ncbi.nlm.nih.gov/datasets/docs/v2/policies-annotation/genome-processing/reference-selection/
Column 6: "taxid"
Taxonomy ID: the NCBI taxonomy identifier for the organism from which the
genome assembly was derived. The NCBI Taxonomy Database is a curated
classification and nomenclature for all of the organisms in the public
sequence databases. The taxonomy record can be retrieved from the NCBI
Taxonomy resource:
https://www.ncbi.nlm.nih.gov/taxonomy/
Column 7: "species_taxid"
Species taxonomy ID: the NCBI taxonomy identifier for the species from which
the genome assembly was derived. The species taxid will differ from the
organism taxid (column 6) only when the organism was reported at a sub-
species or strain level.
Column 8: "organism_name"
Organism name: the scientific name of the organism from which the sequences
in the genome assembly were derived. This name is taken from the NCBI
Taxonomy record for the taxid specified in column 6. Some older taxids were
assigned at the strain level and for these the organism name will include the
strain. Current practice is only to assign taxids at the species level; for
these the organism name will be just the species, however, the strain name
will be reported in the infraspecific_name field (column 9).
Column 9: "infraspecific_name"
Infraspecific name: the strain, breed, cultivar or ecotype of the organism
from which the sequences in the genome assembly were derived. Data are
reported in the form tag=value, e.g. strain=AF16. Strain, breed, cultivar
and ecotype are not expected to be used together, however, if they are then
they will be reported in a list separated by ", /". Empty if no strain,
breed, cultivar or ecotype is specified on the genomic sequence records.
Column 10: "isolate"
Isolate: the individual isolate from which the sequences in the genome
assembly were derived. Empty if no isolate is specified on the genomic
sequence records.
Column 11: "version_status"
Version status: the release status for the genome assembly version.
Values:
latest - the most recent of all the versions for this assembly
chain
replaced - this version has been replaced by a newer version of the
assembly in the same chain
suppressed - this version of the assembly has been suppressed
An assembly chain is the collection of all versions for the same assembly
accession.
Column 12: "assembly_level"
Assembly level: the highest level of assembly for any object in the genome
assembly.
Values:
Complete genome - all chromosomes are gapless and have no runs of 10 or
more ambiguous bases (Ns), there are no unplaced or
unlocalized scaffolds, and all the expected chromosomes
are present (i.e. the assembly is not noted as having
partial genome representation). Plasmids and organelles
may or may not be included in the assembly but if
present then the sequences are gapless.
Chromosome - there is sequence for one or more chromosomes. This
could be a completely sequenced chromosome without gaps
or a chromosome containing scaffolds or contigs with
gaps between them. There may also be unplaced or
unlocalized scaffolds.
Scaffold - some sequence contigs have been connected across gaps to
create scaffolds, but the scaffolds are all unplaced or
unlocalized.
Contig - nothing is assembled beyond the level of sequence
contigs
Column 13: "release_type"
Release type: whether this version of the genome assembly is a major, minor
or patch release.
Values:
Major - changes from the previous assembly version result in a
significant change to the coordinate system. The first
version of an assembly is always a major release. Most
subsequent genome assembly updates are also major releases.
Minor - changes from the previous assembly version are limited to the
following changes, none of which result in a significant
change to the coordinate system of the primary assembly-unit:
- adding, removing or changing a non-nuclear assembly-unit
- dropping unplaced or unlocalized scaffolds
- adding up to 50 unplaced or unlocalized scaffolds which are
shorter than the current scaffold-N50 value
- replacing a component with a gap of the same length
Patch - the only change is the addition or modification of a patch
assembly-unit.
See the NCBI Assembly model web page (https://www.ncbi.nlm.nih.gov/assembly/
model/#asmb_def) for definitions of assembly-units and genome patches.
Column 14: "genome_rep"
Genome representation: whether the goal for the assembly was to represent the
whole genome or only part of it.
Values:
Full - the data used to generate the assembly was obtained from the
whole genome, as in Whole Genome Shotgun (WGS) assemblies for
example. There may still be gaps in the assembly.
Partial - the data used to generate the assembly came from only part of
the genome.
Most assemblies have full genome representation with a minority being partial
genome representation. See the Assembly help web page
(https://www.ncbi.nlm.nih.gov/assembly/help/) for reasons that the genome
representation would be set to partial.
Column 15: "seq_rel_date"
Sequence release date: the date the sequences in the genome assembly were
released in the International Nucleotide Sequence Database Collaboration
(INSDC) databases, i.e. DDBJ, ENA or GenBank.
Column 16: "asm_name"
Assembly name: the submitter's name for the genome assembly, when one was
provided, otherwise a default name, in the form ASM#####v#, is provided by
NCBI. Assembly names are not unique.
Column 17: "asm_submitter"
Assembly submitter: the submitting consortium or first position if a list of
organizations. The full submitter information is available in the NCBI
BioProject resource: www.ncbi.nlm.nih.gov/bioproject/
Column 18: "gbrs_paired_asm"
GenBank/RefSeq paired assembly: the accession.version of the GenBank assembly
that is paired to the given RefSeq assembly, or vice-versa. "na" is reported
if the assembly is unpaired.
Column 19: "paired_asm_comp"
Paired assembly comparison: whether the paired GenBank & RefSeq assemblies
are identical or different.
Values:
identical - GenBank and RefSeq assemblies are identical
different - GenBank and RefSeq assemblies are not identical
na - not applicable since the assembly is unpaired
Column 20: "ftp_path"
FTP path: the path to the directory on the NCBI genomes FTP site from which
data for this genome assembly can be downloaded.
Column 21: "excluded_from_refseq"
Excluded from RefSeq: reasons the assembly was excluded from the NCBI
Reference Sequence (RefSeq) project, including any assembly anomalies. See:
https://www.ncbi.nlm.nih.gov/assembly/help/anomnotrefseq/
Column 22: "relation_to_type_material"
Relation to type material: contains a value if the sequences in the genome
assembly were derived from type material.
Values:
assembly from type material - the sequences in the genome assembly were
derived from type material
assembly from synonym type material - the sequences in the genome assembly
were derived from synonym type material
assembly from pathotype material - the sequences in the genome assembly
were derived from pathovar material
assembly designated as neotype - the sequences in the genome assembly
were derived from neotype material
assembly designated as reftype - the sequences in the genome assembly
were derived from reference material where type material never was
available and is not likely to ever be available
ICTV species exemplar - the International Committee on Taxonomy of Viruses
(ICTV) designated the genome assembly as the exemplar for the virus
species
ICTV additional isolate - the International Committee on Taxonomy of
Viruses (ICTV) designated the genome assembly an additional isolate for
the virus species
Column 23: "asm_not_live_date"
Assembly no longer live date: the date the assembly transitioned from
version_status latest to either replaced or suppressed. When the assembly is
in status latest, "na" is reported.
Column 24: "assembly_type"
Assembly type: the type of assembly, including haploid, haploid-with-alt,
diploid, unresolved-diploid, alternate-pseudohaplotype
Column 25: "group"
Taxonomy Group: commonly used organism groups:
Eukaryota: Animals, Fungi, Plants, Protists;
Prokaryota: group corresponds to phylum;
Viruses: groups defined as the first level (not ranked)
below the kingdom of Viruses
Column 26: "genome_size"
Genome Size: total length of all top-level sequences in the primary
assembly
Column 27: "genome_size_ungapped"
Genome Size - Ungapped length: total length of all top-level sequences
in the primary assembly ignoring gaps. Any stretch of 10 or more Ns in a
sequence is treated like a gap
Column 28: "gc_percent"
GC%: Percent of nitrogenous bases (guanine or cytosine) in DNA submitted
for the assembly, rounded to the nearest 0.5%
Column 29: "replicon_count"
Replicon count: total number of chromosomes, organelle genomes, and
plasmids in the primary assembly
Column 30: "scaffold_count"
Scaffold count: number of scaffolds including placed, unlocalized,
unplaced, alternate loci and patch scaffolds in the primary assembly
Column 31: "contig_count"
Contig count: number of contigs in the primary assembly
Column 32: "annotation_provider"
Annotation provider: the group that provided the annotation on the assembly
Column 33: "annotation_name"
Annotation name: the name of the annotation that is on the assembly
Column 34: "annotation_date"
Annotation date: the date that the assembly was annotated
Column 35: "total_gene_count"
Total gene count: the total number of genes that are annotated on the
assembly. If an assembly has no genes, or is lacking a gene count, it will
display "na". If an assembly has no features but is annotated, then it will
show 0.
Column 36: "protein_coding_gene_count"
Protein coding gene count: the total number of protein coding genes on the
assembly
Column 37: "non_coding_gene_count"
Non-coding gene count: the total number of non-coding genes on the assembly
Column 38: "pubmed_id"
PubMed ID: The PubMed ID(s) that are associated with the assembly,
separated by commas
=====================================
HOW TO USE THE ASSEMBLY SUMMARY FILES
=====================================
The metadata provided in the assembly_summary.txt files can be used to identify
assemblies of interest for subsequent download.
The Genomes FTP FAQ provides examples of how to use the assembly_summary.txt
files to download sets of assemblies. See:
How can I download only the current version of each assembly?
https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#current
How can I download RefSeq data for all complete bacterial genomes?
https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#allcomplete
Other sets of assemblies of interest can be downloaded using variations on
these instructions.
________________________________________________________________________________
National Center for Biotechnology Information (NCBI)
National Library of Medicine
National Institutes of Health
8600 Rockville Pike
Bethesda, MD 20894, USA
tel: (301) 496-2475
fax: (301) 480-9241
e-mail: info@ncbi.nlm.nih.gov
________________________________________________________________________________
This directory contains the following NCBI Taxonomy database dump files:
new_taxdump.zip
new_taxdump.tar.Z
new_taxdump.tar.gz
All these files containes exactly the same information and are arranged so
for the convenience of unpacking them on various operating environments.
In addition there are files:
new_taxdump.zip.md5
new_taxdump.tar.Z.md5
new_taxdump.tar.gz.md5
which contain MD5 sums for the corresponding archive files. These files
might be used to check correctness of the download of corresponding
archive file.
new_taxdump.zip
---------------
Is intended for zip-capable utilities such as pkunzip, unzip, and WinZip.
These utilities are widely available in almost all operating environments.
To unpack it command-line pkunzip and unzip:
pkunzip new_taxdump.zip
or
unzip new_taxdump.zip
Note: pkunzip and/or unzip executables must be in the executable search path
and new_taxdump.zip must be in the current directory. Files will be unzipped into
current directory. For desired dump files placement and more please refer to
the manual and/or option descriptions of pkunzip and unzip utilities.
new_taxdump.tar.Z
-----------------
This file is to be unpacked by uncompress utility and subsequent tar
archiver. These utilities are usually used in UNIX-like environment.
Unpacking instructions follows:
uncompress -c new_taxdump.tar.Z | tar xf -
new_taxdump.tar.gz
------------------
This file is to be unpacked by GNU unzip utility and subsequent tar
archiver. These utilities are usually used in UNIX-like environment.
Unpacking instructions follows:
gunzip -c new_taxdump.tar.gz | tar xf -
The content of the archive
--------------------------
It may look like this:
citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
typeoftype.dmp
merged.dmp
names.dmp
nodes.dmp
host.dmp
typematerial.dmp
rankedlineage.dmp
fullnamelineage.dmp
taxidlineage.dmp
excludedfromtype.dmp
images.dmp
readme.txt
The readme.txt file gives a brief description of *.dmp files. These files
contain taxonomic information and are briefly described below. Each of the
files store one record in the single line that are delimited by "\t|\n"
(tab, vertical bar, and newline) characters. Each record consists of one
or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters.
The brief description of field position and meaning for each file follows.
nodes.dmp
---------
This file represents taxonomy nodes. The description for each node includes
the following fields:
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank -- rank of this node (superkingdom, kingdom, ...)
embl code -- locus-name prefix; not unique
division id -- see division.dmp file
inherited div flag (1 or 0) -- 1 if node inherits division from parent
genetic code id -- see gencode.dmp file
inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
mitochondrial genetic code id -- see gencode.dmp file
inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
comments -- free-text comments and citations
plastid genetic code id -- see gencode.dmp file
inherited PGC flag (1 or 0) -- 1 if node inherits plastid gencode from parent
specified_species -- 1 if species in the node's lineage has formal name
hydrogenosome genetic code id -- see gencode.dmp file
inherited HGC flag (1 or 0) -- 1 if node inherits hydrogenosome gencode from parent
names.dmp
---------
Taxonomy names file has these fields:
tax_id -- the id of node associated with this name
name_txt -- name itself
unique name -- the unique variant of this name if name not unique
name class -- (synonym, common name, ...)
division.dmp
------------
Divisions file has these fields:
division id -- taxonomy database division id
division cde -- GenBank division code (three characters)
division name -- e.g. BCT, PLN, VRT, MAM, PRI...
comments
gencode.dmp
-----------
Genetic codes file:
genetic code id -- GenBank genetic code id
abbreviation -- genetic code name abbreviation
name -- genetic code name
cde -- translation table for this genetic code
starts -- start codons for this genetic code
delnodes.dmp
------------
Deleted nodes (nodes that existed but were deleted) file field:
tax_id -- deleted node id
merged.dmp
----------
Merged nodes file fields:
old_tax_id -- id of nodes which has been merged
new_tax_id -- id of nodes which is result of merging
citations.dmp
-------------
Citations file fields:
cit_id -- the unique id of citation
cit_key -- citation key
medline_id -- unique id in MedLine database (0 if not in MedLine)
pubmed_id -- unique id in PubMed database (0 if not in PubMed)
url -- URL associated with citation
text -- any text (usually article name and authors)
-- The following characters are escaped in this text by a backslash:
-- newline (appear as "\n"),
-- tab character ("\t"),
-- double quotes ('\"'),
-- backslash character ("\\").
taxid_list -- list of node ids separated by a single space
typeoftype.dmp
--------------
Type material types file fields:
type_name -- name of type material type
synonyms -- alternative names for type material type
nomenclature -- Taxonomic Code of Nomenclature coded by a single letter:
-- B - International Code for algae, fungi and plants (ICN), previously Botanical Code,
-- P - International Code of Nomenclature of Prokaryotes (ICNP),
-- Z - International Code of Zoological Nomenclature (ICZN),
-- V - International Committee on Taxonomy of Viruses (ICTV) virus classification.
description -- descriptive text
host.dmp
--------
Theoretical host for organism file fields:
tax_id -- node id
potential_hosts -- theoretical host list separated by comma ','
typematerial.dmp
----------------
Type material information file fields:
tax_id -- node id
tax_name -- organism name type material is assigned to
type -- type material type (see typeoftype.dmp)
identifier -- identifier in type material collection
rankedlineage.dmp
-----------------
Select ancestor names for well-established taxonomic ranks (species, genus, family, order, class, phylum, kingdom, superkingdom) file fields:
tax_id -- node id
tax_name -- scientific name of the organism
species -- name of a species (coincide with organism name for species-level nodes)
genus -- genus name when available
family -- family name when available
order -- order name when available
class -- class name when available
phylum -- phylum name when available
kingdom -- kingdom name when available
superkingdom -- superkingdom (domain) name when available
fullnamelineage.dmp
----------------
Full name lineage file fields:
tax_id -- node id
tax_name -- scientific name of the organism
lineage -- sequence of sncestor names separated by semicolon ';' denoting nodes' ancestors starting from the most distant one and ending with the immediate one
taxidlineage.dmp
----------------
Taxonomy id lineage file fields:
tax_id -- node id
lineage -- sequence of node ids separated by space denoting nodes' ancestors starting from the most distant one and ending with the immediate one
excludedfromtype.dmp
--------------------
A set of strains or vouchers determined not be from type material:
tax_id -- node id
tax_name -- organism name type material is assigned to
property -- "not considered type" for strains/vouchers determined to be wrongly assigned
-- "not verified as type" for strains/vouchers of uncertain provenance
voucher_strain -- strain or voucher id string
Organism images file (images.dmp):
image_id -- the unique id of image
image_key -- image key
url -- image URL associated with citation
license -- image license
attribution -- image attribution
source -- source of the image
properties -- various image properties separated by semicolon
taxid_list -- list of node ids separated by a single space