EBI metagenomics--a new resource for the analysis and archiving of metagenomic data

Abstract

Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.

Figure 1.

Screenshots from the ENA’s Webin tool showing the pages where (a) users select which MIxS checklist they wish to use for the submission and (b) the subsequent list of optional and mandatory fields they can enter values for. Note that a spreadsheet may optionally be used to perform the same task.

Figure 2.

Overview of the pipeline used by EBI metagenomics to process raw sequence files and predict the functions and taxa present in a given sample.

Figure 3.

Screenshots of the analysis results pages where users can visualize the outputs of the analysis pipeline in a number of formats. A pie chart (a) summarizing the OTUs present in the sample is shown by default on the taxonomy results page and users can switch between a bar chart (b), stacked chart (c) and interactive Krona viewer (d) by selecting an icon from the ‘switch view’ menu.