mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

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...

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Autores principales:	Nicholas A. Bokulich, Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, J. Gregory Caporaso
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/aa182d80d78440c2a9049d7390b83256
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spelling	oai:doaj.org-article:aa182d80d78440c2a9049d7390b832562021-12-02T18:15:43Zmockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking10.1128/mSystems.00062-162379-5077https://doaj.org/article/aa182d80d78440c2a9049d7390b832562016-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00062-16https://doaj.org/toc/2379-5077ABSTRACT 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 high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.Nicholas A. BokulichJai Ram RideoutWilliam G. MercurioArron ShifferBenjamin WolfeCorinne F. MauriceRachel J. DuttonPeter J. TurnbaughRob KnightJ. Gregory CaporasoAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmSystems, Vol 1, Iss 5 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Nicholas A. Bokulich Jai Ram Rideout William G. Mercurio Arron Shiffer Benjamin Wolfe Corinne F. Maurice Rachel J. Dutton Peter J. Turnbaugh Rob Knight J. Gregory Caporaso mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
description	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 high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.
format	article
author	Nicholas A. Bokulich Jai Ram Rideout William G. Mercurio Arron Shiffer Benjamin Wolfe Corinne F. Maurice Rachel J. Dutton Peter J. Turnbaugh Rob Knight J. Gregory Caporaso
author_facet	Nicholas A. Bokulich Jai Ram Rideout William G. Mercurio Arron Shiffer Benjamin Wolfe Corinne F. Maurice Rachel J. Dutton Peter J. Turnbaugh Rob Knight J. Gregory Caporaso
author_sort	Nicholas A. Bokulich
title	mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
title_short	mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
title_full	mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
title_fullStr	mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
title_full_unstemmed	mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
title_sort	mockrobiota: a public resource for microbiome bioinformatics benchmarking
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/aa182d80d78440c2a9049d7390b83256
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mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

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