Marine metagenomics is the study of genetic material recovered directly from the sea. It is a new and rapidly expanding area of research, and there is a danger that data is produced faster than users are able to share, analyse and interpret it. There is an urgent need to create a data management infrastructure dedicated to marine research.
This Use Case aims develop a sustainable metagenomics infrastructure to enhance research and industrial innovation within the marine domain. It will provide a web based portal through which researchers can access a marine reference database. The database will be populated with data from the European Nucleotide Archive (ENA), UniProt and other sources.
What the Use Case does
- Develops and implements data standards for the marine domain.
- Develops and implements databases specific to marine metagenomics.
- Evaluates and implements tools and pipelines for metagenomics analyses.
- Develops a search engine for the interrogation of marine metagenomics datasets.
- Organises training workshops for end users.
- EBI metagenomics portal: portal for metagenomics analysis: an automated pipeline for analysing and archiving metagenomic data.
- Marine Metagenomics Portal (MMP) (Beta version)
- MarRef: a database for completely sequenced marine prokaryotic genomes.
- MarDB: a database of sequenced marine prokaryotic genomes regardless of level of completeness.
- MarCat: a catalogue of marine genes and proteins derived from metagenomics samples.
- META-pipe: a marine metagenomics analysis pipeline.
- ITSoneDB: a database for fungal ITS1 sequences
- Standards and best practices: You can view the first publication on best practices in GigaScience. This is a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets.
- Data Resources: You can follow the development of specific marine metagenomics contextual and sequence reference databases, such as MarRef, MarDB and MarCat, at the Marine Metagenomics Portal (MMP). The marine fungal ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences database is at ITSone DB.
- Tools and pipelines to enhance metagenomics analyses: We are developing free resources for the analysis, archiving and browsing of metagenomic and metatranscriptomic data, such as the pipelines EBI-Metagenomics Portal (EMG) analysis service and the marine oriented META-pipe (beta) pipeline.
- Workshops on metagenomics analysis: We organise workshops for end users, such as “Metagenomics data analysis” and “Metagenomics bioinformatics”, where training materials and videos are made available. See the Events page or 'Related Events' section below to find upcoming workshops.
How the Use Case is organised
The Marine Metagenomics Use Case work is carried out by Work Package 6 in the ELIXIR EXCELERATE project. The Work Package is led by Nils Peder Willassen (ELIXIR Norway) and Rob Finn (EMBL-EBI).
Find out more
- Marine Metagenomics Portal community page
- Contact mmp[at]uit[dot]no for any enquiries about the Marine Metagenomics Portal.
- Slides about the Marine Metagenomics Use Case - from the ELIXIR All Hands Meeting, March 2017.
- Webinar about the Marine Metagenomics Pilot Study
- ELIXIR pilot action: Marine Metagenomics – towards a domain specific set of sustainable services: a paper summarising the results of the Pilot Study.
- Use Cases
- ELIXIR-EXCELERATE Work Package 6 on the intranet (you must be logged in)