EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Nucleic Acids Res, 2018/01/04;46(D1):D726-D735.
Mitchell AL[1], Scheremetjew M[1], Denise H[1], Potter S[1], Tarkowska A[1], Qureshi M[1], Salazar GA[1], Pesseat S[1], Boland MA[1], Hunter FMI[1], Ten Hoopen P[1], Alako B[1], Amid C[1], Wilkinson DJ[2], Curtis TP[3], Cochrane G[1], Finn RD[1]
Affiliations
PMID: 29069476DOI: 10.1093/nar/gkx967
Impact factor: 19.16
Abstract
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.
MeSH terms
Algorithms; Base Sequence; Classification; Databases, Genetic; Datasets as Topic; Metagenomics; Microbiota; RNA, Archaeal; RNA, Bacterial; RNA, Viral; Ribotyping; Software; Transcriptome; User-Computer Interface; Web Browser; Workflow
More resources
Full text:
Europe PubMed Central; PubMed Central
EndNote: Download