Last updated:2015.11.6.

Whole Genome Shotgun (WGS) sequences data

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 from the proceeding genome project can be submitted to DDBJ/EMBL-Bank/GenBank as WGS data.
See also INSDC standards for genome assembly submission.

See the list of publicized 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.

Prior to sequence data submission, it is required to submit to BioProject Database and BioSample Database.
DDBJ accepts following two formats for WGS submissions;
a) WGS + scaffold CON:

  • The WGS entries are the contigs (overlapping reads with no gaps)
  • The WGS entries can NOT have consequence "n"'s to represent sequencing gaps.
  • If you need to submit how the WGS entries are assembled together into scaffolds or chromosomes, you can submit AGP file. DDBJ can accept scaffold (assembled contigs separated by gaps) as CON entry", in AGP format.
b) WGS with gaps:

  • The WGS entries are the scaffolds (assembled contigs separated by gaps).
  • The WGS entries can contain consequence "n"'s to represent sequencing gaps.
  • No AGP file is required.

The WGS data are expected to be updated as the project progresses.
When the genome sequencing is completed , the complete sequence(s) will be assigned new accession number(s) constructed with two alphabets and six digits and the WGS accession number will be made secondary.
Then, the complete genome entry will be 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.

Example: ZZZZ01000001

4 letters -- Prefix to distinguish each project
2 digits -- Version number of the data set
6 digits -- ID of each individual sequence (Sometimes, it might be 7 or 8 digits depended on 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
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
  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
FEATURES             Location/Qualifiers
     source          1..123456
                     /mol_type="genomic DNA"
                     /note="contig: A01234B01"
                     /organism="Homo sapiens"

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