Submitting genome assemblies

The European Nucleotide Archive (ENA) is offering a new genome assembly pipeline made available through Webin framework. Although Webin is an interactive tool, the system is designed to support transfers of large data sets. Submissions of several hundred assemblies are well supported. Interactive components of the system lead the user through a set of high-level questions to describe the assembly data, study and sample description steps and a file transfer system to capture the data themselves.

The genome assembly submission steps have been updated on March 31, 2014 to be in line with the new system.

Please note the current pipeline is for submission of new genome assemblies only. If you wish to update an existing genome assembly, please contact datasubs@ebi.ac.uk.

Starting a genome assembly submission

If you have previously submitted to the European Nucleotide Archive (ENA) - either raw reads or assembled and annotated sequences - which means you have an account with ENA you can use the same account details to use the new genome assembly system by logging in to Webin.

If you are new to ENA, you will need to register a submission account with us.

Registering a submission account

Submissions are made through a registered Webin submission account ... more information.

After registration, you will be logged in immediately and can review your account details or proceed with your submission.

There is also a Reset password button that you can use should you ever forget your password and need to reset it.

Preparing files for upload

A genome assembly can comprise a number of layers of information that need to be provided – reads, contigs, scaffolds and chromosomes* – and at the end of the submission process, there will be in place the following 4 components:

  1. Study details (Please read to check when you need to register a new study and how to submit non-study genome assemblies)
  2. Raw read data (Recommended)
  3. At least one of the following: Contig , Scaffold, Chromosome data (Please note: under “chromosome” we include here organelle (e.g. mitochondrion and chloroplast) and plasmid sequences.)
  4. Assembly description files (Required only if chromosome or unlocalised records are being submitted)

Once you have created an account and uploaded your Assembly data in one of the supported data formats you can proceed with the assembly submission. To do so:

  1. Login
  2. Select 'Submit assemblies'
  3. Create a new study (or select an existing one), fill in the required fields (below) and follow the on-screen questions (*)
    • Release date
    • Study short name
    • Study descriptive title
    • Abstract
  4. Create new samples by uploading a spreadsheet or by following the on-screen instructions. At this stage you will be required to add organism details, if your organism can not be found please refer to this page.

(*) If you need a locus tag when you are asked whether you want to provide functional genome annotation you have to say 'Yes'. Locus tag prefixes are only associated to studies providing functional genome annotation.

For any questions, please contact datasubs@ebi.ac.uk.

Detailed reporting requirements on genome assembly submissions are provided here.

Latest ENA news

01 Jul 2015: ENA release 124
Release 124 of ENA's assembled/annotated sequences now available

20 Jun 2015: Sample Checklist Updates - June 2015
ENA are planning to update several sample metadata reporting checklists. Some of these changes have been carried out for harmonisation of attributes/fields between various checklist. Other changes were made to allow a standardised missing/null value reporting. All changes will come into effect as of 3rd August 2015.

03 Jun 2015: Changes to read data submission services 1st of October 2015
ENA will make a number of changes to submission services for raw sequence read data on first of October 2015. We continue to track an ever evolving landscape of available and preferred formats and introduce these changes with a view to overall simplification of the submission system to allow us to provide a more efficient service with faster turnaround.