Mockrobiota: A public resource for microbiome bioinformatics benchmarking

Nicholas A. Bokulich, Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, James G Caporaso

Research output: Contribution to journalArticle

25 Scopus citations

Abstract

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by highthroughput marker gene sequencing.

Original languageEnglish (US)
Article numbere00062
JournalmSystems
Volume1
Issue number5
DOIs
StatePublished - Sep 1 2016

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ASJC Scopus subject areas

  • Molecular Biology
  • Physiology
  • Genetics
  • Biochemistry
  • Modeling and Simulation
  • Computer Science Applications
  • Ecology, Evolution, Behavior and Systematics
  • Microbiology

Cite this

Bokulich, N. A., Rideout, J. R., Mercurio, W. G., Shiffer, A., Wolfe, B., Maurice, C. F., Dutton, R. J., Turnbaugh, P. J., Knight, R., & Caporaso, J. G. (2016). Mockrobiota: A public resource for microbiome bioinformatics benchmarking. mSystems, 1(5), [e00062]. https://doi.org/10.1128/mSystems.00062-16