EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Nucleic Acids Res. 2018 Jan 4;46(D1):D726-D735. doi: 10.1093/nar/gkx967.


EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Classification / methods
  • Databases, Genetic*
  • Datasets as Topic
  • Metagenomics* / methods
  • Microbiota*
  • RNA, Archaeal / genetics
  • RNA, Bacterial / genetics
  • RNA, Viral / genetics
  • Ribotyping
  • Software
  • Transcriptome
  • User-Computer Interface
  • Web Browser
  • Workflow


  • RNA, Archaeal
  • RNA, Bacterial
  • RNA, Viral