mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
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DOI：
10.1128/msystems.00062-16
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发表时间：
2016-09-01
期刊：
影响因子：
6.4
通讯作者：
Caporaso, J. Gregory
中科院分区：
文献类型：
--
作者：
Bokulich, Nicholas A.;Rideout, Jai Ram;Caporaso, J. Gregory
模拟群落是验证、优化和比较微生物群落分析的生物信息学方法的重要工具。我们提出mockrobiota，一个公共资源共享，验证和记录模拟社区数据资源，可在http://caporaso-lab.github.io/mockrobiota/。mockrobiota中包含的材料包括数据集和样本元数据，预期的组成数据（分类或基因注释或模拟社区成员的参考序列），以及原始数据的链接（例如，原始序列数据）。mockrobiota不直接提供实物样本材料，但为每个模拟社区提供的数据集元数据表明是否有实物样本材料。在撰写本文时，mockrobiota包含11个模拟社区数据集与已知的物种组成，包括细菌，古细菌和真核生物模拟社区，通过高通量标记基因sequencing.IMPORTANCE分析的标准和公共模拟社区数据的可用性将促进正在进行的方法优化，跨研究的比较，共享源数据，更大的透明度和访问，并消除冗余。这些也是生物信息学教学和培训的宝贵资源。这个动态资源旨在扩展和发展，以满足组学社区不断变化的需求。
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.