################################################################################ 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 1, 2016 ################################################################################ ====================== 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. ===================== COLUMN SPECIFICATIONS ===================== 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: http://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: http://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: http://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: http://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: http://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 (http://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 (http://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. ===================================== 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? http://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#current How can I download RefSeq data for all complete bacterial genomes? http://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 ________________________________________________________________________________