News

2015-04-23New: Attention for alphabetical sorting of BioSamples submitted from D-way

After submitting BioSamples from D-way, BioSamples are sorted in alphabetical (ASCII code) order of sample_name values and NOT in order of appearance (top to bottom in tab-delimited text file). BioSample accession numbers are issued to the alphabetically-sorted BioSamples.

Please enter sample_name values as such their "order of appearance" and "alphabetical order" to be same.

Since the sample_name is used as the identifier in database system, it cannot be changed after submission. Submitters can name sample by using the sample_title attribute. The sample_title is used as a title in public record and can be updated.

sample_names contain serial numbers

Following samples are sorted as intended.

0001_control
0002_a sample
0003_b sample

Following examples are NOT sorted as intended (sorted by first letters).

1_control
5_a sample
10_b sample
->
1_control
10_b sample
5_a sample

DDBJ is developing the database system to preserve order of appearance (top to bottom in tab-delimited text file). If you have questions, please contact us from here.

2015-03-11: Users are able to submit BioProject/BioSample/DRA at once

New BioProject, BioSample and DRA submission system were released at 8th, April (Wed).

This system enhancement was carried out by funding from MEXT Genome Science.

Tutorial video. [youtube id="Hg4h8ytbIV4" title="Submission to BioProject, BioSample and DRA"]

DRA Handbook

The new system is able to reference and submit BioProject, BioSample and DRA submissions which had been registered in the former system.

BioProject, BioSample and DRA data can be submitted at once

Before submission to DRA, BioProject and BioSample accession numbers were required. In the new system, BioProject, BioSample and DRA data can be submitted at once, so submitters need not to wait for BioProject and BioSample accession numbers.

Experiment and Run which are same number of BioSample, are automatically created. Submitter and hold action in the DRA submission are copied to "SUBMITTER" of BioProject and BioSample.

BioProject and DRA data can be submitted at once
BioSample and DRA data can be submitted at once

Registered BioSample attributes text file is available in D-way

Users can download the registered BioSample attributes text file in D-way (blue box). Updates will be reflected to the file.

Download sample attribute file

Reference sequence of bam can be specified by accession number

Reference sequence in single fasta file was required to submit alignment data in bam.

In the new system, if references are found in ftp://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/, references can be specified by their accession numbers.

In the DRA submission tool, "BioSample Used" was moved

In the DRA submission tool, "BioSample Used" was moved from rightmost to just right to "Experiment Alias", which enables users to easily understand relationship between "Experiment" and "referencing BioSample".

BioSample Used is moved to just right to Experiment Alias

Fastq from capillary sequencing platforms can be submitted to DRA

In the DRA submission tool, capillary sequencing platforms can be selected. Fastq from these platforms can be submitted to DRA. To submit sequence chromatgrams, please continue to submit data to DDBJ Trace Archive.

  • AB 3730xL Genetic Analyzer
  • AB 3730 Genetic Analyzer
  • AB 3500xL Genetic Analyzer
  • AB 3500 Genetic Analyzer
  • AB 3130xL Genetic Analyzer
  • AB 3130 Genetic Analyzer
  • AB 310 Genetic Analyzer

Sequencing instruments were added

In the DRA submission tool, following Illumina and Oxford nanopore sequencers were added.

  • HiSeq X Ten
  • NextSeq 500
  • MinION
  • GridION

PacBio hdf5 file can be submitted

PacBio hdf5 file can be submitted. Select "PacBio_HDF5" for Run File Type.

"Illumina_native", "Illumina_native_qseq" and "Helicos_native" are removed from Run filetype

"Illumina_native", "Illumina_native_qseq" and "Helicos_native" are removed from Run filetype. These types can be specified in XML.

Other changes

  • BioProject and BioSample Submitting organizations are pre-entered with "Lab/Group", "Department (2)", "Department (1)", "Organization" of D-way account. Text in the submitting organization can be editted.
  • BioSample "Private comments to DDBJ staff" was moved from "COMMENTS" tab to "GENERAL INFO". "COMMENTS" tab was removed.

DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive.