Genome assemblies including metagenomes can be submitted to the European Nucleotide Archive (ENA) through the interactive Webin service. Note that this service supports the submission of a large number of assemblies. Genome assembly submissions include plasmids, organelles, complete virus genomes, viral segments/replicons, bacteriophages, prokaryotic or eukaryotic genomes in any assembly layer (contigs/scaffolds/chromosomes).
The following picture illustrates the stages of the genome assembly submission process:
Register the Study. You must provide a description of your sequencing study. For this, please follow here either the interactive Webin or the programmatic Webin study submission guidelines. Note that the study and the sample are independent objects in the ENA metamodel and are only coupled once sequences are submitted.
Register the Sample. You must describe the physical sequenced sample providing the associated metadata (organism, strain, collection date, etc). This is done by using the appropiate sample checklist. To register a sample, please follow here either the interactive Webin or the programmatic Webin sample submission guidelines. Note that the study and the sample are independent objects in the ENA metamodel and are only coupled once sequences are submitted.
Prepare the files.
You must prepare your files in a specific format in order for them to be processed by the genome assembly pipeline.
Please see Genome Assembly Data Formats for the file formats used for genome assembly submissions.
Note that all the files must be gz compressed. Providing the correct format is a critical step for your submission to be completed automatically.
Upload files.
You must upload data files into your Webin upload area before you can submit them using Webin. Once the files have been submitted they will be moved from the Webin upload area into the archive.
Please see Data Upload for full details on how to upload data files.
Define the Assembly. During the submission process in the ENA interactive Webin service, the interface will automatically indicate the files to be uploaded based on your answer to a short multiple choice questionaire (3 questions). Please answer the questions carefully and be sure to upload the right files. This is a critical step for your submission to be completed automatically.
Submit the Assembly. Once you successfully submit your assembly, you will see in Webin a confirmation page in your browser; submission account holders will also receive a confirmation email providing a unique identifier for each submitted assembly (ERZXXXXXX). This identifier should be used to contact us for any further query related to the submission. The ERZXXXXXX must not be used in the sequence citation paper. Accession numbers to be used for publication purposes are described here.
Once you have registered your ENA Webin account, you can follow the below instructions to submit a genome assembly. We strongly suggest to visit the interactive Webin service before preparing the files to become familiar with the submission tool.
New submitters are required to register a Webin submission account. Once you have an ENA Webin account, please log in here.
- Once you have logged into your ENA Webin account, start the genome submission by selecting the New Submission tab and clicking the 'Submit genome assemblies' option.
- To continue with the next step, click 'Next'.
- Select the study that you will be adding the genome assembly to. If the study that you want to submit to does not exist yet you can create one now (red asterisk). However, it is best to split your submission up and create the study as part of an earlier session.
- Click next to move to the next stage. The next stage is the sample registration stage. In most cases the samples will have already been registered (it is best to submit the samples in a separate submission so that the work is more divided). If the sample has aleady been registered, find the ‘skip’ option to skip this step. If the samples do not exist, do not use the skip option, you can create some samples during this step.
- Please answer carefully the 3 given questions to determine which files are required for your assembly submission. The default submission (all answers NO) allows the submission of contigs/scaffolds in fasta format.
QUESTION 1: Are the sequences assembled into chromosomes or replicons? The chromosomes do not need to be fully sequenced, there can be assembly gaps. If you have assembled plasmids, organelles, bacteriophage genomes or viral segments, please submit them as 'chromosomes' by answering YES to this question.
QUESTION 2: Does the assembly contain scaffolds or chromsomes described using an AGP file? If you have an AGP file mapping either scaffolds from contigs (scaffold AGP) or chromosomes from scaffolds (chromosome AGP), you should submit them as such and we will build the corresponding sequence(s).
QUESTION 3: Are the sequences functionally annotated? You need to provide information about the existence of functional annotation. This will determine if a Fasta file or a EMBL flat file should be submitted.
- If your assembly contains assembled chromosomes, there will be an additional question to determine if you plan to submit unlocalised sequences. Unlocalised sequences are contigs or scaffolds that are associated with a specific chromosome but their order and orientation is unknown.
- You must provide here the accession number (ERSXXXXXX) of the sample to be associated with this assembly. You can also provide the unique name (or alias) of the sample.
- You must fill up the assembly information.
- Following your answers in the section 1., this section of the right panel will indicate the files to be submitted. The default submission (all answers NO) allows the submission of contigs/scaffolds in fasta format. You must provide here the file names (files must be already uploaded) and also the MD5 checksum for each file. All files must be gz compressed. If they are not, please upload them again before continuing. Note that you will be able to submit only one file of each type:
One Fasta or EMBL flat file with the sequence(s)
One AGP file
One chromosome list file
One unlocalised list file
Therefore, if you wish to submit both scaffolds and chromosomes without AGP file, please submit all the sequences in the same file (either Fasta or EMBL flat file depending if there is functional annotation or not); you will be requested to submit as well a chromosome list file that will identify the chromosome sequences. Likewise, if you wish to submit contig sequences plus an AGP file to build scaffolds and an AGP file to build chromosomes, you must merge both AGP and submit them as one AGP file only.
- You can also provide the above information in a spreadsheet file. You can download/upload the template in this section.
- Once all the above information is provided, please proceed to the next step.
In this page you will be able to add more assemblies with similar information.
- Select here how many assemblies you wish to submit (from 1 to 199) and click '+Add'. The list of assemblies will be displayed. You can navigate throught the list either by selecting them in the list or using the buttons in the right panel (see red asterisk).
- Please provide the information for each assembly by editing each one of them accordingly. Note that each assembly must have a unique sample so you must change at least the sample accession number, the file names and checksum for each assembly. Once you fill up the information in a given field, a green button will indicate that is completed (not necessarily validated).
- You can also download the provided information in a spreadsheet file template by clicking the button 'Download Spreedsheet".
- Once all the information is carefully provided and all fields are indicated with green buttons, you will be able to submit the assembly/assemblies by clicking the "Submit" button. The system will validate the information provided at this stage and display an error message if there are issues to be corrected.
Once your assembly has been successfully received at ENA (although not processed yet), you will see in your browser a confirmation page similar to the one above. A confirmation email will be also sent to all submission account holders.
This submission confirmation means that the sequences, functional annotation if applicable, study and sample information, assembly information, etc. will be processed all together in order for the final genome assembly to be displayed in the database according to the release date specified in the study. If no errors are detected, submission account holders will receive in few days an automatic email with the sequence accession numbers. Otherwise, the account holders will be contacted by email to make the necessary corrections. Please note that the error processing is done manually and may take longer than expected. Please take that into consideration if you have a publication deadline. We strongly suggest our submitters to make all efforts to follow up these instructions closely in order to complete your assembly submission automatically. You are welcome to contact us prior submission if you need to do so (datasubs@ebi.ac.uk).
Thank you for submitting to ENA.