EBI metagenomics

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About EBI Metagenomics

EBI Metagenomics service


Metagenomics is the study of all genomes present in any given environment...

Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. For example, in its simplest form, a metagenomic study might be the direct sequence results of DNA extracted from a bucket of sea water.

The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.

Please take your time to explore and tell us what you think about our website. We welcome your feedback on look and feel, functionality or scientific content. If you want to be kept informed about updates to the website, please subscribe to our mailing list. Also note, as we constantly try to improve the site, it may change from time to time.

Why choose EBI Metagenomics?

Easy submission

easy submission

The EBI Metagenomics service offers a manually-assisted submission route, with help available to ensure data and metadata formatting comply with the European Nucleotide Archive (ENA) data schema and the Genomic Standards Consortium (GSC) sample metadata guidelines respectively, allowing harmonisation of analysis efforts across the wider genomics community.

Powerful analysis

powerful analysis

The service identifies rRNA sequences, using rRNASelector, and performs taxonomic analysis upon 16S rRNAs using Qiime. The remaining reads are submitted for functional analysis of predicted protein coding sequences using the InterPro sequence analysis resource. InterPro uses diagnostic models to classify sequences into families and to predict the presence of functionally important domains and sites. By utilising this resource, the service offers a powerful and sophisticated alternative to BLAST-based functional metagenomic analyses.

Data archiving

data archiving

Data submitted to the EBI Metagenomics service is automatically archived in the European Nucleotide Archive (ENA). Accession numbers are supplied for sequence data as part of the archiving process, which is a prerequisite for publication in many journals. The ENA only accepts data that is intended for public release. However, any data submitted to us can be kept confidential (by secure user login) for a period of up to 2 years to allow time for the data producer to publish their findings. It should be noted that ALL data must eventually be suitable for public release.

How to use EBI Metagenomics for data analysis

Register with us

Registration is required to submit data for analysis. Please note that the registration system is shared with ENA, so if you have previously submitted sequences to EMBL-Bank you will already have a valid account.

Check your data format

The service accepts all NGS shotgun sequence reads, including Roche 454, Illumina and IonTorrent sequences, from metagenomic or metatranscriptomic samples. Amplicon marker gene studies may be included, particularly if they are associated with other meta-omic data for a sample.

If your dataset does not fit these descriptions, please contact us to help us better understand your needs.

Filter any human-associated samples

Human associated samples (e.g., human gut samples) must be filtered prior to submission to remove any human contaminants.

How we analyse the data

The latest version of the pipeline includes the following steps:

Raw reads
Initial reads
Processed reads
ncRNA selection
Reads with rRNA & tRNA masked
ORF predictions
Predicted CDS
Functional analysis
IPR matches & GO terms
Reads with rRNA
16s rRNA
Taxonomic analysis
OTUs & taxonomic lineage
Reads with tRNA

Please find here more detail about the pipeline tools & steps that were used to analyse our data.

How to cite

To cite EBI Metagenomics, please refer to the following publication:

Alex Mitchell, Francois Bucchini, Guy Cochrane, Hubert Denise, Petra ten Hoopen, Matthew Fraser, Sebastien Pesseat, Simon Potter, Maxim Scheremetjew, Peter Sterk and Robert D. Finn (2015).
EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Research (2015) doi: 10.1093/nar/gkv1195

View previous citations

Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra Gonzalez-Beltran, Christopher Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radhakrishnan, Philippe Rocca-Serra, Maxim Scheremetjew, Peter Sterk, Daniel Vaughan, Guy Cochrane, Dawn Field and Susanna-Assunta Sansone (2013).
EBI metagenomics - a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Research (2013) doi: 10.1093/nar/gkt961



The EBI metagenomics resource was initiated by funding from EMBL. It continues to be developed with support from EMBL and additional funding has been gratefully received from the Biotechnology and Biological Sciences Research Council (BBSRC grant BB/I02612X/1 and BB/M011755/1) and the EU's Seventh Framework Programme for Research (FP7 grant MICROB3).

Follow us

If you would like to be kept informed of further developments with the EBI metagenomics resources please follow us on Twitter using @EBImetagenomics.


We would like to thanks our beta testers for providing valuable feedback.

The team

This new resource for metagenomics is supported by the EBI Metagenomics Team, in collaboration with the ENA and UniProt groups.


We would like to thank the following authors for their contribution related to the pictures used on the website:

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