mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.
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.IMPORTANCEThe 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.
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
Nicholas A
NA
Bokulich
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
Jai Ram
JR
Rideout
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
William G
WG
Mercurio
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
Arron
A
Shiffer
Department of Biology, Tufts University, Medford, Massachusetts, USA.
Benjamin
B
Wolfe
Department of Microbiology & Immunology Department, Microbiome and Disease Tolerance Centre, McGill University, Montreal, Quebec, Canada.
Corinne F
CF
Maurice
Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.
Rachel J
RJ
Dutton
Department of Microbiology and Immunology, GW Hooper Foundation, University of California, San Francisco, San Francisco, California, USA.
Peter J
PJ
Turnbaugh
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA; Department of Pediatrics, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA.
Rob
R
Knight
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
J Gregory
0000-0002-8865-1670
JG
Caporaso