Acceptable data for DDBJ
For the request of primary entry submission, in principle, DDBJ accepts any nucleotide sequences that are experimentally determined by submitters, but can not accept computational predicted and/or cited sequences.
Even if your sequence is identical to previously reported sequence(s), on the condition that the sequence is independently determined, you can submit it as a "new" entry.
DDBJ also acccepts an entry that is obtained by assembling primary entries publicized from INSDC (DDBJ/EMBL-Bank/GenBank) and/or is added annotation(s) by experimental or inferential method by submitter as TPA (third party annotation).
When you are to publicize raw output data for your studies related to SNPs, WGS, transcriptome and so on, we recommend you to contact with DDBJ Trace Archive (DTA) or DDBJ Read Archive (DRA), instead of DDBJ/EMBL-Bank/GenBank.
Submisson of the data including identical sequences or partially duplicated sequences
Basically, DDBJ accepts all sequence data that are independently determined, even though seqences are identical each other. For variation studies, DDBJ also accepts submissions of representative data.
If you determine many sequences derived from the same indivisual, we strongly recommend to update sequence data submitted previously, rather than to submit new sequence data many times. However, since multicycle submissions for a single resource are required by any reasons; right for sequence data, phases of sequencing etc., DDBJ does not restrict them.
DDBJ Trace Archive (DTA)
DDBJ Trace Archive (DTA) is a repository of DNA sequence chromatograms (traces), base calls, and quality estimates from various large-scale sequencing projects.
DTA is collecting trace data in a collaboration with Trace Archive (NCBI) and Ensembl Trace Server (EBI) in a part of INSDC.
You can search, browse and download trace data submitted to DTA from DTA Search. You can also transfer any trace data submitted to DTA from FTP Site.
DDBJ Read Archive (DRA)
DDBJ Read Archive (DRA) is collecting output data generated by next-generation sequencing methodologies sucn as 454, Solexa, SOLiD and so on.
DRA is a member of collaboration with Short Read Archive (NCBI) and European Read Archive (EBI) in a part of INSDC.
"Raw" output or fastq data without any processing (removal of adapter sequence, filtering etc.) are required for DRA submission.