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MGnify: the microbiome analysis resource in 2020.

Alex L Mitchell1, Alexandre Almeida1,2, Martin Beracochea1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nucleic Acids Research
|November 8, 2019
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Summary
This summary is machine-generated.

MGnify has enhanced its microbiome data platform with new analysis pipelines for improved reproducibility and expanded functional annotations. The resource now offers advanced tools for taxonomic and pathway analysis, supporting over a billion protein sequences.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • MGnify is a public platform for microbiome data analysis and archiving.
  • The platform has doubled its analyzed datasets in the past two years.
  • Previous analysis relied on a single, less adaptable pipeline.

Purpose of the Study:

  • To introduce MGnify version 5.0 with updated analysis pipelines.
  • To enhance data provenance, reusability, and reproducibility.
  • To expand taxonomic and functional annotation capabilities.

Main Methods:

  • Implementation of multiple, data-tailored analysis pipelines using Common Workflow Language.
  • Inclusion of taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2).
  • Addition of expanded protein functional annotations and biochemical pathway predictions for assembled contigs.

Main Results:

  • A six-fold increase in assembled and analyzed datasets.
  • A non-redundant protein database exceeding one billion sequences.
  • Development of a new contig viewer for detailed visualization of assembled contigs and annotations.

Conclusions:

  • MGnify v5.0 offers a more robust and versatile platform for microbiome research.
  • Enhanced analytical capabilities improve the depth and reliability of microbiome data interpretation.
  • The platform's growth and new features support a rapidly expanding field of microbiome science.