Submitting a Bacteriophage Genome to ENA – Part 1

Due to the complicated nature of submitting a genome to the European Nucleotide Archive (ENA), we have written this guide on submitting a bacteriophage genome in an attempt to make the process much smoother.

1. Register a Submission Account

To submit sequences to the ENA, you must have a submission account. Details on how to register for an account can be found at:

2. Register a Study

Every submission to the ENA must belong to a study. Studies are used to group together data submissions all belonging to a common project.

To register a study, login to the Webinar submission service at:

Go to the “New Submission” tab, select “Register Study (project)” and click next.

Fill out all the mandatory fields (marked *) on the form that appears, ensuring to mark “Yes” for the part asking, “In this study, will you provide functional genome annotation?”. In the box that appears underneath, enter locus tag prefixes for any genomes you wish to submit to this study. Locus tags are used to name every gene in a genome systematically, as below:

FT   CDS             1..100
FT                   /locus_tag="PHAGE_00001"
FT   CDS             101..200
FT                   /locus_tag="PHAGE_00002"

In the above example, the locus tag prefix is “PHAGE”. Each genome you want to submit must have its own unique locus tag prefix.

Click submit to register the study.

After a study has been successfully registered, it will appear under the “Studies” tab where you can find the Primary Accession for the study (beginning with PRJEB) which you will need further on to submit your data.

3. Taxonomy Request

To submit a novel phage genome, you will also need to request a a new taxa ID. To do this, go to the “New Submission” tab and select “Taxonomy Check/Request”.

Enter the proposed names for the phage genomes you wish to submit and click “Send details” to request a taxa ID.

4. Register a Sample

Every submission must also be associated with a sample. While the study represents the whole project to which the sequences belong, the sample represents the source of the material of the sequencing data. For example, the raw reads and the genome assembly of an organism would be two separate submissions belonging to the same sample. If you wanted to submit data for a different organism belonging to the same project, you would have to register a new sample under the same study.

Go to the “New Submission” tab on the Webin submission service, select “Register samples” and click next.

Click “Select checklist” and you will be prompted to select an appropriate checklist. The simplest and most basic method to register a sample is to select the “Ena default sample checklist” under “Other Checklists”. Click next.

On this page, you can select any fields describing your samples or add a custom field if there is information you wish to add that is not covered by any of the existing fields. Using this checklist, all fields are optional and you don’t have to select any. Click next.

The next page doesn’t require you to input any information so click next.

On this page, enter the number of samples you wish to register and click add. Multiple different samples can be registered to a study at this stage, provided they all require the same checklist selected above.

For each of the samples, fill out the mandatory fields (marked *). The “Unique Name” for a sample is used internally to differentiate between different submissions of the same data for the same organism (e.g. different assemblies of the same genomes, different isolates of the same organism). The Unique Name cannot be changed after submission. Use the search bar to search for the taxa ID you requested above and select the organism that appears. If nothing appears upon entering your taxa ID, it may not have been processed yet and you should contact the ENA.

Click submit and the next page will present you with the “Primary Sample Accession” numbers of all the samples, each beginning with ERS.

After the samples have been successfully registered, they will appear under the “Samples” tab where you can find the the Primary Accessions needed futher on to submit your data.

Note, a sample only becomes associated with a study after you have submitted your data specifying the study and sample.