About

The MGnify service

MGnify 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). The MGnify resource was previously known as EBI Metagenomics, but was re-branded in 2018 to reflect its growing remit.

What does MGnify offer

Powerful analysis

MGnify offers multiple analysis pipelines that are tailored according to input data (amplicon, raw read or assembly), providing (where appropriate) detailed taxonomic and functional analysis of microbiome sequence data.

Access to an extensive selection of analysed data

MGnify houses a vast repository of analysed microbiome datasets, processed using standardized pipelines and workflows, allowing analyses to be placed in context with other studies from similar environments.

Programmatic access to analysed data

In addition to visualisations available from the website and downloadable results files, MGnify analyses can be queried and retrieved via a RESTful API, giving full programmatic access to the data.

Archiving of user-submitted data

Through partnership with the European Nucleotide Archive (ENA), user-submitted sequence data and metadata is archived. Accession numbers are supplied as part of this process, which is a prerequisite for publication in many journals.

Standards-compliant data

Submission tools help ensure sequence data and metadata comply with ENA data schemes and the Genomic Standards Consortium (GSC) metadata guidelines, allowing harmonisation of analysis efforts across the wider genomics community.

Funding

Current funding: MGnify currently receives funding support from: the European Union’s Horizon 2020 Research and Innovation programme (817729, 862923, and 952914) and Research Infrastructures programme (824087); the Biotechnology and Biological Sciences Research Council (BB/S009043/1, BB/T000902/1, BB/V01868X/1, and BB/W002965/1); ELIXIR, the research infrastructure for Life-Science data; EMBL – FNR (CORE International); and European Molecular Biology Laboratory (EMBL) core funds.

Previous funding: MGnify was initiated with institutional funding from EMBL. It gratefully acknowledges previous funding received from the Biotechnology and Biological Sciences Research Council (BB/M011755/1 and BB/I02612X/1), the European Union’s Horizon 2020 Research and Innovation programme (676559 and 654008), Innovate UK (102513) and the European Union’s Seventh Framework Programme for Research (287589).

How to cite

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

MGnify v5.0 | MGnify: the microbiome analysis resource in 2020. Doi: 10.1093/nar/gkz1035 | A Mitchell, A Almeida, M Beracochea, M Boland, J Burgin, G Cochrane, M R Crusoe, V Kale, S C Potter, L J Richardson, E Sakharova, M Scheremetjew, A Korobeynikov, A Shlemov, O Kunyavskaya, A Lapidus, R D Finn. | Nucleic Acids Res 48(D1):D570-D578 (2020).

Contact

If you would like to get in touch, please contact us using the helpdesk. We will respond as quickly as possible, but bear in mind that we do not have a member of staff dedicated to running the helpdesk service.

Please, check our FAQs. prior to contacting us.

If your questions relate to submission of sequence data and/or metadata, please contact the (ENA helpdesk) who are responsible for this providing the submission services.

News and updates

If you would like to keep up to date with developments within MGnify, please follow us on Twitter (@MGnifyDB).

Service status

The service status page <https://status.mgnify.org/>_ lists any known issues and outages.