These are the submission instructions for prokaryotic and eukaryotic genome submissions.

• If you are submitting a viral genome, please see your submission options.
• Do not submit organelle genomes here unless as part of a genome assembly. If you are only submitting organelle genomes, submit them in BankIt.
• MAGs: To submit prokaryotic or eukaryotic Metagenome-assembled Genomes (MAGs), see the MAG instructions.

• For detailed instructions see the Prokaryotic and Eukaryotic Genomes Submission Guide.

Each sequence in the genome submission must be at least 200 base pairs and less than the technical limit of 2,147,483,000 base pairs (roughly 2^31). Write to genomes@ncbi.nlm.nih.gov if your genome assembly includes sequences longer than that limit.

Sequences cannot be randomly concatenated.

Submissions have either FASTA files or ASN ( .sqn ) file formats, not a mix of file types.

• Choose the FASTA format (.fsa) if you do not have feature annotations
• Choose the ASN format (.sqn) if you want to include feature annotation or the Genome-Assembly-Data structured comment

If you have assignment information:

• For single genome submissions, provide information on which sequences belong to chromosomes, plasmids, or organelles.
• Additional requirements for Batch and Haplotype submissions

Users have the optional opportunity to request PGAP (only relevant for prokaryotic genomes).

See Genome‘s Frequently Asked Questions page.

There are three types of Genome submissions: Single, Batch, and Pseudohaplotypes/Haplotypes.

• Click for detailed information on Submitting a Single Genome

• Submitting up to 400 genomes that have some common information
• Click for detailed information on Submitting a Batch of Genomes

All genomes within a batch must:

• Have the same BioProject
• Be either WGS or non-WGS, not a mix of both types
• Have the same (initial) release date
• Have the same gap/Ns information
• Have either FASTA files or ASN ( .sqn ) files, not a mix of file types
  • Choose FASTA files if you do not have feature annotations
  • Choose ASN files if you want to include feature annotation or the Genome-Assembly-Data structured comment
• One file for each genome
  • One file for all the sequences of that genome
  • For example, a batch submission of 2 genomes would have 2 files

• Submitting the haplotype assemblies generated from one or more diploid genomes.
• Click for detailed information on Submitting Multiple Haplotype Assemblies

The haplotypes of a particular individual genome must:

• Meet the same restrictions as Batch submissions listed above, except each must have their own BioProject that will be connected by an Umbrella BioProject. These BioProjects can be automatically created during the genome submission. See Umbrella BioProject for information.
• All haplotypes use the same BioSample of the individual that was sequenced

The pseudohaplotypes/haplotype pairs will be asserted as one of the appropriate types:

• principal/alternate
• maternal/paternal
• haplotype 1/haplotype 2

All genome submissions must provide BioProject and BioSample information, which can be created before or during a genome submission.

Submitting with Feature Annotation: If you are planning to submit with feature annotation with locus-tag prefix, you must create a BioProject and BioSample before you start Genome submission. See Annotation at left for more information.

A BioProject contains the description of the research effort, relevant grant(s), and links to the public data. It has a BioProject accession. See BioProject for more information.

A genome must belong to a BioProject. Genomes sequenced as part of the same research effort can belong to a single BioProject.

• Use the same BioProject for the sequence reads and genome assembly made from those reads; do not create duplicate BioProjects.
• Exception: Haplotypes of a diploid genome have different BioProjects, which can be created during pseudohaplotype/haplotype submission.

A BioSample contains the source information of the sample sequenced. It has a BioSample accession. See BioSample for more information.

• Use the same BioSample accession for the sequence reads and genome assembly made from those reads; do not create duplicate BioSamples.
• Exception: Metagenome Assembled Genomes (MAGs) need a BioSample for each individual organism bin. The reads are submitted using a BioSample that represents the mixed sample (i.e. soil metagenome or host name). See the MAG instructions.

Feature annotation is optional for genomes submissions.

• Please upload only the FASTA file on the Files tab.
• During submission, you can request to have prokaryotic genomes annotated by NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP).

• Click for information on How to Submit an Annotated File.
• Click for information on GFF3 or GTF annotation.
• If you decide to submit a genome with feature annotation, it must contain the locus-tag prefix generated for you so that your genes are uniquely identifiable.

1. Create a BioProject submission. Make sure the 'autogenerate locus tag prefix' checkbox is selected on the Project Type page of your BioProject submission.
2. Create the BioSample submission and enter the corresponding BioProject accession into the sample metadata.
3. After you finish your BioSample submission, the automatically assigned locus_tag prefixes will be posted to the BioProject submission portal. Should you not receive the autogenerated locus tag prefix, please email genomes@ncbi.nlm.nih.gov
4. Create your Genome submission

Please prepare the following information to submit as metadata (Detailed information available here):

• Assembly method: Name of the assembly algorithm(s)
• Assembly method version or date
• Genome coverage
• Sequencing technology or technologies
• Full or Partial Genome in the sample
• Reference genome if it is not a de novo assembly
• When updating, include the accession of the genome being updated

• If there is no feature annotation, upload FASTA file(s)
• If there is feature annotation, upload an ASN format (.sqn file)

• Filename: Filenames including extension must exactly match the filenames provided on the Genome info tab.

• File upload via the web interface using HTTP or Aspera Connect browser plugin
• FTP and Aspera upload. See How to Preload Files for details

After completing your submission, the genomes will undergo several validations plus an initial review by our staff. See What Happens Next for details.

• Automatic emails will be sent to the email account associated with the submission. These automated emails will include our contact information if you have any questions.

The following is a list of Genome possible submission statuses:

• Queued: the submission is waiting for initial review.
• Error: one or more genomes has errors in its files, so needs to be resubmitted. Use the same file name when resubmitting batch submissions.
• Processing (no accession number): all the genomes that have passed the initial automated validations and are waiting for additional review.
• Processing (with accession number): genome accessions have been assigned and the genomes will be processed by NCBI staff. Genomes will remain at this status until they are released. We will contact you during processing if the submission has issues that require additional information.
• Processed: the genome has been publicly released.

The submission portal reflects a static image of the information at time of submission. Any requested changes after submission will not be reflected on the submission portal.