Submitting (meta)genome assemblies

The European Nucleotide Archive (ENA) is offering a new genome and metagenome 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 (meta)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 and metagenome assemblies only. If you wish to update an existing genome assembly, please contact

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

Detailed reporting requirements on genome assembly submissions are provided here.

Latest ENA news

12 Jul 2017: Submission service maintenance - 14/7/17 to 17/7/17

Webin submission services will not be available between Friday 14/7...

07 Jul 2017: Update to Aspera server

EBI has built a new Aspera server on up-dated hardware with the latest Aspera version and configuration. This should improve...

06 Jul 2017: ENA Release 132

Release 132 of ENA's assembled/annotated sequences now available

30 Jun 2017: Taxon support for sequence, WGS and assembly in ENA Browser Tools

You can now download sequence, WGS and assembly data by tax ID using ENA Browser Tools

23 Jun 2017: New tools to download data from ENA

Introducing two new tools to make retrieving data from ENA much easier: enaBrowserTools and ENA FTP Downloader.