The EBI Metagenomics service

EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).

What does EBI Metagenomics offer

Standards-compliant data
The service provides submission tools that help ensure sequence data and metadata comply with the European Nucleotide Archive (ENA) data schemes and the Genomic Standards Consortium (GSC) metadata guidelines, allowing harmonisation of analysis efforts across the wider genomics community.
Powerful analysis
The service provides powerful taxonomic and functional analysis of sequence data. Functional analysis results can be summarized and compared using Gene Ontology (GO) terms.
Data Archiving
Data submitted to the service is automatically archived in the ENA. Accession numbers are supplied for sequence data as part of the archiving process, which is a prerequisite for publication in many journals.
Programmatic access to the data
Data deposited in the service are discoverable and queryable via RESTful API using unique URLs constructed from accession numbers supplied during archiving process.


EBI Metagenomics was initiated with funding from EMBL. It continues to be developed with EMBL support and funding gratefully received from the Biotechnology and Biological Sciences Research Council (BBSRC grant BB/M011755/1) and [ELIXIR GRANT INFO]. It previously received funding from BBSRC grant BB/I02612X/1 and the EU’s Seventh Framework Programme for Research (FP7 grant MICROB3).

How to cite

If you find this resource useful, please consider citing the following publication:

A Mitchell, M Scheremetjew, H Denise, S Potter, A Tarkowska, M Qureshi, G A Salazar, S Pesseat, M A Boland, F M I Hunter, P ten Hoopen, B Alako, C Amid, D J Wilkinson, T P Curtis, G Cochrane, R D Finn.
Nucleic Acids Research (2017) Database Issue 46:D726–D735. 10.1093/nar/gkx967 (PDF)


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