SP-GenBank offers four major workflows, organized by sequenced material: (1) Prokaryote, (2) Eukaryote, (3) Virus, and (4) Synthetic construct. Some sequence types have features automatically annotated.

Table: Overview of the types of assembled sequences to submit to SP-GenBank () or elsewhere, as noted below.

Raw, unassembled reads from next generation sequencing: submit to SP-SRA.

If none of the above describes your data, see more options. You may also contact us.

Checklist of what you will need for your submission:

1. Submitter contact details, authors, publication, data release date
2. Sequencing technology (e.g. Sanger, Illumina)
3. Nucleotide sequences
4. Sequence source information (e.g. organism, collection_date)
5. Feature annotation
   • Features are automatically annotated for specific submissions, including SARS-CoV-2, Influenza, Dengue virus, Norovirus, metazoan COX1, rRNA, and rRNA-ITS.
   • For other submission types, you will need to provide feature annotation.

Before you begin your submission, you will need to sign in to NCBI using the Log in button on the upper right side of the SP-GenBank page.

Prepare a plain text file containing sequences in FASTA format. FASTA format starts with a definition line followed with a hard return and the sequence. The simplest definition line requires the ">" symbol and a sequence_ID, like the example below.

Example:

>Seq1
CCTTTAT...
>Seq2
GGTAGGT...

Keep sequence_IDs short, simple, and without spaces. More information on FASTA format.

In one submission, you can upload a single FASTA file that contains up to 3,000 sequences. However, if your sequences are long (e.g. chloroplast genomes), prepare a FASTA file with fewer sequences and make separate submissions as needed.

All submissions should include information about the biological or environmental source of the sequences, including organism name and descriptive details such as collection_date, geo_loc_name ( geographic location), etc. You will enter relevant source information by typing directly into a table within the Submission Portal or by uploading a tab-delimited text file.

• organism: species name of the organism (e.g. Oryza sativa, Hepacivirus hominis). You may provide a higher-level taxonomic node if you cannot identify the organism to the species level (e.g. Lactobacillaceae bacterium). Organism names will be checked against the Taxonomy database, and for unrecognized organisms, you may be presented with additional forms to complete.
• Source identifiers distinguish each sequence in a submission file. These include:
  • isolate (all organism groups)
  • strain (prokaryotes and viruses)
  • clone (prokaryotes and sometimes for synthetic constructs)
  • specimen_voucher (eukaryotes)
• collection_date and geo_loc_name (geographic location) are required for prokaryote, eukaryote, and viruses.
• host and/or isolation_source are required for viruses and some prokaryotes.

You can use optional identifiers as appropriate for your submission.

GenBank features are biological elements present in a sequence, such as coding regions, promoters, rRNAs, etc. Annotation is the process of applying the features to your sequences.

• Automatic feature annotation (no submitter features required): Features are automatically applied for specific submission types, including SARS-CoV-2, Influenza, Dengue virus, Norovirus, metazoan COX1, rRNA, and rRNA-ITS. You do not need to annotate features for these submissions.
• Submitter provided feature annotation: For submission types not listed above, there are three ways to provide annotation:
  • Complete a form during submission
  • Create and upload a 5-column tab-delimited feature table
  • Create and upload protein FASTA file to annotate CDS features

After completing your submission, it will undergo processing at GenBank. Processing includes automated validations and manual review by NCBI staff. Various reports will be sent to the email accounts associated with the submission, including copies of your processed submission. The amount of time to go from submitted to processed status varies.

You can monitor the status of your submission in SP-GenBank. Some of the submission statuses are:

• Error: the submission has errors that you need to fix before accession numbers can be assigned.
• Processing: the submission is undergoing an initial review by our staff before assigning accession numbers.
• Processing (accession numbers assigned): the submission is undergoing final review by NCBI staff. We will contact you if we require additional information.
• Processed (accession numbers assigned): the submission has gone through all processing steps at GenBank and is ready for public release.

Any changes requested after processed status will be incorporated into your GenBank records, however these changes will not be shown in Submission Portal. For information on updating processed records, see the GenBank update page.

Submit your sequence data on desktop. The desktop view allows you to easily:

• Enter your information
• Enter or upload metadata
• Upload large source files
• Review your submission

Email me a link to get started