The whole genome shotgun approach (the whole genome is once blasted into millions of fragment, which are sequenced and reassembled to produce a series of sequence 'scaffolds'.) has been used to sequence the genome of various organisms.
The large set of contigs or the finished sequences without annotation from the proceeding genome project can be submitted to DDBJ/EMBL-Bank/GenBank as WGS data.
You can submit WGS data to DDBJ via Mass Submission System (MSS).
Acceptable WGS data
In principle, DDBJ/EMBL-Bank/GenBank can accept assemblies (i.e. overlapping reads) that are appropriately assembled sequences and can not accept redundant reads (i.e. raw read sequences). If you wish to publicize raw read sequences, we recommend you to contact with DDBJ Trace Archive (DTA) or DDBJ Sequence Read Archive (DRA), instead of DDBJ/EMBL-Bank/GenBank.
To describe on your paper or other purpose, submitted WGS data should be open to the public* with their accession numbers.
* You can specify a hold-date for your WGS data.
See also Principle of "Hold-Until-Published" data release .
- Any assemblies can not have consequence "n" s representing sequencing gap.
- DDBJ can accept assembled sequences separated by gaps (i.e. supercontigs) as contigs of assemblies, "scaffold CON entry", in the AGP file format.
- Further contig structures, ultra-scaffold and/or chromosomal can also be submitted as CON entries in the AGP file format.
- Prior to sequence data submission, get a BioProject ID for your project on the BioProject Database
The WGS data are expected to be updated as the project progresses. When the genome sequencing is completed but not annotated with appropriate features, i.e. CDS (protein-coding gene) and others, the data are still processed as WGS. After addition of feature annotation, the complete genome sequence is assigned a new accession number constructed with two alphabets and six digits and the WGS accession number is made secondary. Then, the complete genome entry is moved to Taxonomic Division classified by the source organism.
WGS accession number
The accession number assigned to each WGS data consists of 4 letters + 8 (sometimes 9 or 10, if necessary) digits.
- 4 letters -- Prefix to distinguish each project
- 2 digits -- Version number of the data set
- 6 digits -- ID of each individual sequence (It sometimes be 7 or 8 digits according to the number of entries.)
The set_version goes up for every update of the dataset. Example: ZZZZ02000001
Sample flat file of WGS data
LOCUS ZZZZ01000001 123456 bp DNA linear HUM 01-MAY-2003 DEFINITION Homo sapiens DNA, chromosome 7, contig: A01234B01. ACCESSION ZZZZ01000001 ZZZZ01000000 VERSION ZZZZ01000001.1 DBLINK BioProject:PRJDA12345 Sequence Read Archive:DRR012345, DRR012346 KEYWORDS WGS. SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 123456) AUTHORS Mishima,H. and Shizuoka,T. TITLE Direct Submission JOURNAL Submitted (01-APR-2003) to the DDBJ/EMBL/GenBank databases. Contact:Hanako Mishima National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan REFERENCE 2 AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Human whole genome shotgun sequence JOURNAL Unpublished (2003) COMMENT ##Genome-Assembly-Data-START## Finishing Goal :: Finished Current Finishing Status :: High Quality Draft Assembly Method :: Newbler v. 2.3 Genome Coverage :: 30x Sequencing Technology :: 454/Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..123456 /db_xref="taxon:9606" /chromosome="7" /mol_type="genomic DNA" /note="contig: A01234B01" /organism="Homo sapiens" -- The rest is snipped -- //