Submitting environmental sequences

This covers the submission of data derived from the sequencing of DNA or RNA from organisms that have not been isolated and is typically focused on entire microbial communities, size fractionated organisms, enrichments cultures and flow sorted microbes. Both amplicon (metabarcoding, diversity survey) and shotgun (metagenomics/metatranscriptomics) based methods are included here.

Minimally, ENA aims to capture and present both raw data and identifications (taxonomic or functional) from environmental sequencing approaches. Additionally, intermediate information, such as mappings between raw reads and identifications and cluster information can also be captured.


There are currently two different Webin submission systems that both should be used for submitting this type of data.  The first should be used for registering samples and submitting raw sequencing reads, the latter is used to submit the assembled and annotated sequences.

Submitting reads and samples

The read domain Webin submission tool (see here) should be used to submit both raw sequencing reads and samples. Minimal sample description should be provided in this step as more detailed MIMARKS compliant information will be provided in the next step while submitting the annotated sequences. Take note of the sample accession as this will be needed during the sequence submission.

Submitting annotated marker sequences

Annotated marker sequences should be submitted using the sequence Webin submission tool:

  1. Register samples (see above)
  2. Login or register
  3. Create a new sequence submission
  4. Select MIMARKS-Survey 16S rRNA sequences
  5. Provide release date
  6. Provide citation details
  7. Choose appropriate fields
  8. Fill the selected fields for each sequence being submitted either manually or by uploading a pre-prepared spreadsheet or a Fasta file
  9. Please note that Sample accessions should be provided in the Sample Accession field

After submission, please wait for contact from curators with any queries or a list of assigned sequence accession numbers with instructions on how to access and cite the submitted data.


The ENA archives Next Generation Sequencing data from metagenomics and metatranscriptomics studies into the read domain. Comprehensive instructions on read data submission can be found here. These guidelines include both programmatic and interactive submissions.

Submitting metagenome assemblies

Metagenome assemblies (contigs, scaffolds and chromosomes) shall be submitted via the ENA (Meta)Genome Assembly Pipeline. A detailed guide on how to submit genomic and metagenomic assemblies is available here.

Sample contextual data

For all studies, but especially metagenomics and metatranscriptomics studies, it is essential that the read data files, study and sequencing experiment description are accompanied by minimal sample metadata information in order to ensure that the data originating from the study are reproducible, meaningful and can be sufficiently analysed.

Minimal reporting requirements for samples of metagenomics and metatrancriptomics studies are addressed in the MIxS data standard described here.

Metagenomic data analysis

Sequencing experiments correctly annotated as metagenomic and containing adequate sample contextual data are eligible for analysis by the EBI Metagenomics services. For further information please contact the EBI metagenomics team directly.