EBI Metagenomics Portal - Towards a better understanding of community metabolism

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Metagenomics is a rapidly expanding field, where modern sequencing technologies are applied to the DNA isolated from an environment, such as soil, seawater or animal gut. This allows us to analyse the DNA from the collection of microorganisms that inhabit the environment, many of which may not have previously been sequenced due to their fastidious nature, making it difficult to culture them in the laboratory. Substantial amounts of sequencing data are produced, which typically only reflect a small fraction of the total DNA. However, after analysis, this DNA provides clues to the taxonomic diversity and functional potential that is found in that environment. Metagenomics is an exemplar of what is referred to as data-driven biology. The cost of DNA sequencing has fallen rapidly, such that most research groups have access to affordable institutional sequencing facilities. We now run the risk of each research group producing its own metagenomics analysis platform and storage repository. To help prevent such a fragmented situation, and to help reduce overall costs (both computational and staff), we have developed and implemented a centralised pipeline to provide a metagenomics data analysis and archiving platform. The EBI Metagenomics Portal (EBI-MP) has been developed as a collaborative UK effort at the EMBL-European Bioinformatics Institute (EMBL-EBI). The portal was launched in 2011 and has increasingly become established as a world leader in metagenomic analysis. Users submit their high-throughput metagenomic nucleotide sequence data, accompanied by contextual data describing their samples and experiments in a controlled and consistent manner. Once analysed by the portal, results including taxonomic and functional annotations can be visualised alongside project and sample descriptions, and can be downloaded for further analysis. In order to keep up with community needs, and to help cement the UK's position as a leader in the field of metagenomics research, the proposed project aims to further develop the portal. This will include the addition of analysis provenance, to ensure that analyses can be re-run in the future as new and updated tools and algorithms become available, without overwriting existing analysed data, which may form the basis of an existing publication. Further enhancements include extending the taxonomic and functional analyses to achieve a better picture of the microbial communities sampled, their composition and biological functions. The portal will also be developed to allow more sophisticated searches of its data, so that users can discover samples or environments based on the kind of microbe or protein function found there. We will also add the ability to perform statistically rigorous cross-sample comparisons, that will allow analysis results from different samples to be compared in a scientifically meaningful way, and provide visualisation tools for such comparisons. With today's modern sequencing technologies producing ever more data, better data compression is essential to speed up data transfer both into EBI-MP and internally within the resource. To this end, we will implement industry-standard compression data structures that have developed at EMBL-EBI.