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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:
ftp://ftp.ncbi.nlm.nih.gov/genomes
Last updated: February 25, 2018
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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 ftp://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:
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
ftp://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:
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
ftp://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.
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COLUMN SPECIFICATIONS
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The assembly_summary.txt files have 20 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 or representative genome
in the NCBI Reference Sequence (RefSeq) project classification.
Values:
reference genome - a manually selected high quality genome
assembly that NCBI and the community have
identified as being important as a standard
against which other data are compared
representative genome - a genome computationally or manually selected
as a representative from among the best
genomes available for a species or clade that
does not have a designated reference genome
na - no RefSeq category assigned to this assembly
Prokaryotes may have more than one reference or representative genome per
species. For more information see:
https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#referencegenome
Eukaryotes have no more than one reference or representative genome per
species. If there are no assemblies in RefSeq for a particular eukaryotic
species, then the GenBank assembly that RefSeq would select as the best
available for that species will be designated as the representative genome.
Viruses may have one or more reference genomes per species. The
representative genome designation is not applied to viruses and viroids.
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: "submitter"
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 proxytype material - the sequences in the genome assembly
were derived from proxytype material
assembly designated as neotype - the sequences in the genome assembly
were derived from neotype material
assembly from reference material - 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
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HOW TO USE THE ASSEMBLY SUMMARY FILES
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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
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