mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Titlemockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.
Publication TypeJournal Article
Year of Publication2016
AuthorsBokulich, NA, Rideout, JRam, Mercurio, WG, Shiffer, A, Wolfe, B, Maurice, CF, Dutton, RJ, Turnbaugh, PJ, Knight, R, J Caporaso, G
JournalmSystems
Volume1
Issue5
Date Published2016 Sep-Oct
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.

DOI10.1128/mSystems.00062-16
Alternate JournalmSystems
PubMed ID27822553
PubMed Central IDPMC5080401