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 create a submission account with us.

Creating an account

To create a submission account please go here, click on the 'Register' button, fill in the form and press the 'Register' button at the end of the page again to complete the registration. You will be logged in immedaitely and can review/change your account details or start 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

24 Sep 2014: ENA Release 121
Release 121 of ENA's assembled/annotated sequences now available.

20 Aug 2014: Read data through Globus GridFTP
Read data can now be downloaded using Globus GridFTP through ebi#ena Globus Online public endpoint.

18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

1 Jul 2014: ENA release 120
Release 120 of ENA's assembled/annotated seqences now available

23 May 2014: Change to date format for advanced search
From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).