MGnify: the microbiome analysis resource in 2020 - PubMed (original) (raw)

. 2020 Jan 8;48(D1):D570-D578.

doi: 10.1093/nar/gkz1035.

Alexandre Almeida 1 2, Martin Beracochea 1, Miguel Boland 1, Josephine Burgin 1, Guy Cochrane 1, Michael R Crusoe 3, Varsha Kale 1, Simon C Potter 1, Lorna J Richardson 1, Ekaterina Sakharova 1, Maxim Scheremetjew 1, Anton Korobeynikov 4, Alex Shlemov 4, Olga Kunyavskaya 4, Alla Lapidus 4, Robert D Finn 1

Affiliations

MGnify: the microbiome analysis resource in 2020

Alex L Mitchell et al. Nucleic Acids Res. 2020.

Abstract

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Figures

Figure 1.

Figure 1.

Krona plots showing ITS-based taxonomic analysis results for sequencing run ERR2237853 from agricultural soil. Panel A shows the analysis results obtained using the UNITE database and B shows those produced with ITSoneDB. These plots are integrated into the taxonomy tab within the analysis results section,

https://www.ebi.ac.uk/metagenomics/analyses/MGYA00383253#taxonomic

.

Figure 2.

Figure 2.

Screenshot showing the percentage completion for a series of KEGG pathways based on the presence of KEGG orthologues,

https://www.ebi.ac.uk/metagenomics/analyses/MGYA00383254#path-systems

.

Figure 3.

Figure 3.

The MGnify contig viewer allows visualization of functional annotation of contigs,

https://www.ebi.ac.uk/metagenomics/analyses/MGYA00383254#contigs-viewer

. In this particular view, the contig ERZ477576.854-NODE-854-length-9986-cov-4.0004:1-9986 has been selected and the proteins coloured according to the COG category, with the four cytochrome c subunits highlighted.

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