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

20 Citations (Scopus)

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

Fingerprint

Benchmarking
bioinformatics
benchmarking
Microbiota
Bioinformatics
Computational Biology
Metadata
Resources
metadata
resource
Genes
Taxonomies
Chemical analysis
sampling
microbial communities
gene
taxonomy
microbial community
species diversity
genetic markers

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., ... Caporaso, J. G. (2016). Mockrobiota: A public resource for microbiome bioinformatics benchmarking. mSystems, 1(5), [e00062]. https://doi.org/10.1128/mSystems.00062-16

Mockrobiota : A public resource for microbiome bioinformatics benchmarking. / Bokulich, Nicholas A.; Rideout, Jai Ram; Mercurio, William G.; Shiffer, Arron; Wolfe, Benjamin; Maurice, Corinne F.; Dutton, Rachel J.; Turnbaugh, Peter J.; Knight, Rob; Caporaso, James G.

In: mSystems, Vol. 1, No. 5, e00062, 01.09.2016.

Research output: Contribution to journalArticle

Bokulich, NA, Rideout, JR, Mercurio, WG, Shiffer, A, Wolfe, B, Maurice, CF, Dutton, RJ, Turnbaugh, PJ, Knight, R & Caporaso, JG 2016, 'Mockrobiota: A public resource for microbiome bioinformatics benchmarking', mSystems, vol. 1, no. 5, e00062. https://doi.org/10.1128/mSystems.00062-16
Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF et al. Mockrobiota: A public resource for microbiome bioinformatics benchmarking. mSystems. 2016 Sep 1;1(5). e00062. https://doi.org/10.1128/mSystems.00062-16
Bokulich, Nicholas A. ; Rideout, Jai Ram ; Mercurio, William G. ; Shiffer, Arron ; Wolfe, Benjamin ; Maurice, Corinne F. ; Dutton, Rachel J. ; Turnbaugh, Peter J. ; Knight, Rob ; Caporaso, James G. / Mockrobiota : A public resource for microbiome bioinformatics benchmarking. In: mSystems. 2016 ; Vol. 1, No. 5.
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